Instytut Fizyki Polskiej Akademii Nauk

Division of Theoretical Physics

Institute of Physcis
Polish Academy of Sciences

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Masovian Symposium on Quantum, Optical and Atomic Physics (MaSQOT)

The symposium took place in Warsaw at IF and CFT PAN from June 10 to 11, 2024.

It was an opportunity for the local physics community to become acquainted with the recent developments and results, exchange experiences and ideas as well as to explore new directions and initiate future collaborations among researchers working in the Masovian region.

Group photo of MaSQOT 2024 participants.

We look forward to seeing you next time!

More information about the meeting can be found on the website,


Condensed matter

Ab initio methods
Bogusławski Email View details Załuska-Kotur Email Website View details
Dynamics of growth processes
Załuska-Kotur Email Website View details Chabowska Email View details
Surface formation
Załuska-Kotur Email Website View details Chabowska Email View details
Quantum dots
Semiconductor surfaces
Topological insulators
Non-Hermitian physics

Fundamental problems of Quantum Theory

Open quantum systems
Quantum–classical transition
Measurement problem
Szańkowski Email View details
Interpretations of quantum theory
Szańkowski Email View details
Wave dark matter
Simulation methods for large quantum systems

Ultra-cold atoms & molecules

Atomic physics with anitmatter (CERN)
Bose–Einstein condensates
Degenerate fermionic matter
Phase space and C-field methods
Few-body problems
Optical lattices
Pauli crystals
Quantum droplets
Integrable models
Bose–Fermi mixtures

Low-dimensional Crystalline Structures

Lead by
Ryszard Buczko Email Website View details Magdalena A. Załuska-Kotur Email Website View details
Research topics
Semiconductor surfaces
Topological insulators
Dynamics of growth processes
Surface formation
Pauli crystals
Many-body correlations
Ab initio methods

Quantum Gases Group

Lead by
Mariusz Gajda Email Website View details
Research topics
Quantum simulators
Bose–Einstein condensates
Degenerate fermionic matter
Many-body correlations
Optical lattices
Pauli crystals
Quantum droplets
Open quantum systems
Quantum–classical transition
Light–matter interactions
Phase space and C-field methods
Bose–Fermi mixtures

Polariton Group

Lead by
Michał Matuszewski Email Website View details
Research topics
Topological insulators
Light–matter interactions
Machine learning
Quantum simulators
Open quantum systems
Quantum electrodynamics

Few Body Problems Group

Lead by
Tomasz Sowiński Email Website View details
Research topics
Quantum simulators
Atomic physics with anitmatter (CERN)
Few-body problems
Many-body correlations
Optical lattices
Light–matter interactions
Pauli crystals
Bose–Einstein condensates

Spin Qubit Group

Lead by
Łukasz Cywiński Email Website View details
Research topics
Open quantum systems
Spin qubits
Quantum dots
Quantum–classical transition

Quantum Noise Group

Lead by
Piotr Deuar Email Website View details
Research topics
Fluid dynamics
Bose–Einstein condensates
Phase space and C-field methods
Quantum droplets
Many-body correlations
Simulation methods for large quantum systems
Cavity hybrid systems
Cavity bosons
Integrable models
Wave dark matter

Ultracold Atoms and Beyond

Lead by
Emilia Witkowska Email Website View details
Research topics
Quantum metrology
Bose–Einstein condensates
Many-body correlations
Optical lattices


prof. dr hab. Zofia Z. Białynicka-Birula Email View details prof. dr hab. Piotr P. Bogusławski Email View details prof. dr hab. Ryszard R. Buczko Email Website View details prof. dr hab. Mariusz M. Gajda Email Website View details prof. dr hab. Perła P. Kacman prof. dr hab. Mai M. Suan S. Li Email Website View details prof. dr hab. Michał M. Matuszewski Email Website View details prof. dr hab. Jan J. Mostowski Email Website View details prof. dr hab. Tomasz T. Sowiński Email Website View details prof. dr hab. Magdalena M. A. A. Załuska-Kotur Email Website View details

Sorry, there are no upcomming seminars at this time.

June 25, 2024
prof. Tommaso Roscilde
ENS Lyon, France
"Let the good entanglement roll: quantum correlations and their dynamics in quantum simulators"

Entanglement is what makes many-body systems special. It is the key aspect of their enormous informational content, which implies a seemingly insurmountable hardness in simulating them; but also a whole new world of possibilities for storing and transforming information with them. In this talk I will discuss how multipartite entanglement–i.e. the most collective form of entanglement–can be produced by the non-equilibrium dynamics of lattice spin models, realized experimentally in several platforms of quantum simulation. I shall discuss the role of connectivity of the interactions among spins (i.e. the range of interactions, and the number of dimensions); and of the nature of elementary excitations, which fundamentally establish entanglement with their dynamics. In turn, I will discuss how the spectrum of the elementary excitations can be read from the time-dependent dynamics, suggesting a new form of spectroscopy for synthetic quantum matter. Our theoretical results will be presented in parallel with experimental ones obtained in Rydberg-atom arrays, representing one of the most promising platforms to explore many-body entanglement.

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June 18, 2024
prof. dr hab. Tomasz Sowiński Email Website View details
Institute of Physics, Polish Academy of Sciences
"Spectroscopy of antiprotonic atoms"

Several high-precision experiments at the Antiproton Decelerator complex at CERN aim to look for any significant differences between matter and antimatter. One of these experiments is AEḡIS, whose primary goal is to test the weak equivalence principle for antimatter by measuring (with atomic accuracy) the free fall of a neutral antihydrogen atom in the Earth's gravitational field. It turns out that the experimental setup and techniques developed at AEḡIS, when expanded appropriately, can be used to produce on-demand complex bound states of matter and antimatter, and then to study their spectroscopic properties. One such natural direction is the possibility of producing neutral antiprotonic atoms, i.e., atoms in which one of the electrons is substituted by almost 2,000 times heavier antiproton. During my talk, I will present how this research can contribute to a better understanding of the bound states of matter and antimatter, as well as the internal structure of atomic nuclei, and how it could potentially become yet another opportunity for precise testing of fundamental theories.

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May 21, 2024
dr Michał Parniak
CENT, University of Warsaw
"Rydberg atom quantum sensing"

Rydberg atoms are an established platform for quantum technologies, with new applications still emerging. Large dipole moment of Rydberg atoms allows for their well-known interacting properties, facilitating e.g. quantum gates. The same property also allows for detection of external fields, using transitions between two Rydberg states. Remarkably, these properties hold even in hot-atom vapor cell systems. I will present our results on detecting as well as transducing microwave and terahertz radiation into the optical domain. I will also discuss sensitivity limits, and show how we can achieve detection of thermal radiation, also in cryogenic conditions. I will also hint at ongoing cold-atom based experiments aimed at demonstrating ultimate quantum-metrological limits of sensing via collective qubit lifetime-extension techniques inspired by our past experiments with quantum memories. Those approaches hold a promise to realise optimal sensing protocol, towards reaching the standard quantum limit.

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May 14, 2024
dr Mircea Trif, prof. IFPAN
Institute of Physics, Polish Academy of Sciences
"Cavity magnonics with domain walls in insulating ferromagnetic wires"

Magnetic domain walls (DWs) are topological defects that exhibit robust low-energy modes that can be harnessed for classical and neuromorphic computing. However, the quantum nature of these modes has been elusive thus far. Using the language of cavity optomechanics, we show how to exploit a geometric Berry-phase interaction between the localized DWs and the extended magnons in short ferromagnetic insulating wires to efficiently cool the DW to its quantum ground state or to prepare nonclassical states exhibiting a negative Wigner function that can be extracted from the power spectrum of the emitted magnons. Moreover, we demonstrate that magnons can mediate long-range entangling interactions between qubits stored in distant DWs, which could facilitate the implementation of a universal set of quantum gates. Our proposal relies only on the intrinsic degrees of freedom of the ferromagnet, and can be naturally extended to explore the quantum dynamics of DWs in ferrimagnets and antiferromagnets, as well as quantum vortices or skyrmions confined in insulating magnetic nanodisks.

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May 7, 2024
Mr. Midhun Anila
Institute of Physics, Polish Academy of Sciences
"Multi-scale simulations of galectin-3"

Intrinsically disordered proteins (IDPs) at physiological conditions have no well-defined, stable structure in extended parts of their polypeptide chains. They participate in many processes in biological cells, including signaling, cell-cycle regulation, and initiation of translation.
IDPs are major components of biomolecular condensates (BCs) that form through liquid-liquid phase separation in biological cells. Despite considerable research on BCs in the cytosol and nucleus, their behavior at cellular membranes remains largely unexplored.
Galectin-3 is a protein comprising an intrinsically disordered N-terminal domain (NTD) and a well-folded carbohydrate recognition domain (CRD) which can bind to glycosphingolipids on the cell membrane. Galectin-3 is known to mediate clathrin-independent endocytosis [1] and has been recently shown to undergo liquid-liquid phase separation [2], but the function of the BCs of galectin-3 in the endocytic pit formation is unknown.
Using dissipative particle dynamics (DPD) simulations, we explore how polymer models resembling galectin-3 sense and respond to membrane curvature. Our findings suggest a generic mechanism by which BCs sense membrane curvature, potentially influencing such cellular processes as endocytosis [3]. To elucidate the conformational dynamics of galectin-3, we have conducted molecular dynamics simulations using the Martini 3 force field. Following the method introduced by Thomasen et al. [4] for rescaling protein-water interactions, we generate a conformational ensemble in good quantitative agreement with data from small angle X-ray scattering experiments [5]. Our simulations reveal large-scale fluctuations between compact and extended conformations of galectin-3, with aromatic residues within the NTD forming most frequent contacts [6].

[1] Lakshminarayan, R., Wunder, C., Becken, U., Howes, M. T., Benzing, C., Arumugam, & Johannes, L. (2014). Galectin-3 drives glycosphingolipid-dependent biogenesis of clathrin-independent carriers. Nature Cell Biology, 16(6), 592-603.
[2] Chiu, Y. P., Sun, Y. C., Qiu, D. C., Lin, Y. H., Chen, Y. Q., Kuo, J. C., & Huang, J. R. (2020). Liquid-liquid phase separation and extracellular multivalent interactions in the tale of galectin-3. Nature Communications, 11(1), 1229.
[3] Anila, M. M., Ghosh, R., & Różycki, B. (2023). Membrane curvature sensing by model biomolecular condensates. Soft Matter, 19(20), 3723-3732.
[4] Thomasen, F. E., Pesce, F., Roesgaard, M. A., Tesei, G., & Lindorff-Larsen, K. (2022). Improving Martini 3 for disordered and multidomain proteins. Journal of Chemical Theory and Computation, 18(4), 2033-2041.
[5] Lin, Y. H., Qiu, D. C., Chang, W. H., Yeh, Y. Q., Jeng, U. S., Liu, F. T., & Huang, J. R. (2017). The intrinsically disordered N-terminal domain of galectin-3 dynamically mediates multisite self-association of the protein through fuzzy interactions. Journal of Biological Chemistry, 292(43), 17845-17856.
[6] Anila, M. M., Rogowski P., & Różycki, B. (2024). Scrutinising the conformational ensemble of the intrinsically mixed-folded protein galectin-3. Under review.

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April 23, 2024
dr hab. Łukasz Cywiński Email Website View details
Institute of Physics, Polish Academy of Sciences
"Quantum computing with silicon quantum dots"

Classical computers are made from semiconductors, but semiconductor-based architectures for quantum computers are still less developed than those based on superconducting circuits, trapped ions, or neutral atoms. I will try to convince you that there are good reasons to still pursue the "semiconductor path" to quantum computers, and discuss challenges that need to be overcome on this path. I will also discuss what kinds of interesting physical problems from solid state physics and open quantum system physics one can grapple with, while contributing to a somewhat "engineering-like" task of building a scalable quantum computer.

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April 16, 2024
dr hab. Karol Szałowski
University of Łódź, Faculty of Physics and Applied Informatics, Department of Solid State Physics
"Tailoring proximity effects in graphene-based van der Waals heterostructures with charge density waves and magnetism in TaS2 and NbS2"

Proximity effects constitute a highly promising tool for versatile engineering of the band structure of graphene in van der Waals heterostructures [1]. Particularly promising relevant systems are based on transition metal dichalcogenides [2]. In the paper some approaches to tune the proximity effects in reversible manner will be discussed. A main one is based on charge density wave degree of freedom. Such a low-temperature ordering is known to develop in 1T polytypes of TaS2 and NbS2, enabling to manipulate the band structure of heterostructures in twistronic-like way without physical alteration of the twist angle.
In the paper the DFT calculations-based predictions of proximity effects in graphene band structure emerging in heterostructures with TaS2 [3] and NbS2 and controllable with charge density wave ordering will be presented. Moreover, magnetism in TaS2 [4] will be discussed as yet another mechanism capable of shaping the proximity effects. Also the external electric field will be demonstrated to be an additional useful factor influencing the band structure.
The interpretation of the results will be based on symmetry-based tight-binding Hamiltonians [3]. Special emphasis will be put on proximity-induced Rashba spin-orbit coupling parametrized by characteristic energy and tuneable angle (inducing possible anisotropic Rashba–Edelstein effect).

Acknowledgements: Financial support provided by the University of Łódź under Grant No. 1/IDUB/DOS/2021 is gratefully acknowledged. Polish high-performance computing infrastructure PLGrid (HPC Centers: ACK Cyfronet AGH) is gratefully acknowledged for providing computer facilities and support within computational grant no. PLG/2023/016571.

[1] J. F. Sierra, J. Fabian, R. K. Kawakami, S. Roche and S. O. Valenzuela, Nature Nanotechnology 16 (2021) 856.
[2] M. Gmitra and J. Fabian, Physical Review B 92 (2015) 155403.
[3] K. Szałowski, M. Milivojević, D. Kochan and M. Gmitra, 2D Materials 10 (2023) 025013.
[4] I. Lutsyk, K. Szałowski et al., Nano Research 16 (2023) 11528.

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April 9, 2024
dr Paweł Krupa Email View details
Institute of Physics, Polish Academy of Sciences
"Computational Studies of Environmental Effects on the Structure and Dynamics of Proteins"

The function of most proteins is strictly connected to their structure, which depends on their sequence and external factors, such as the surrounding environment. Interactions of proteins with lipid bilayers, for example, can significantly affect both systems and strongly depend on the lipid composition. This presentation will focus on demonstrating how external factors can impact protein structure and dynamics, examined through molecular dynamics simulations. I will present examples of several protein systems in bulk water, as well as when interacting or embedded into lipid bilayers of various compositions and how environmental conditions and other factors, such as the presence or absence of disulfide bonds, can influence them.

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March 26, 2024
dr Karol Gietka
Institut für Theoretische Physik, Universität Innsbruck
"Singular quantum Fisher information matrix in critical metrology"

Critical metrology relies on the extreme sensitivity of the system's eigenstates close to the critical point to Hamiltonian parameter perturbations. Typically, however, the critical point, at which the phase transition occurs, is a function of many if not all the parameters of the system. This suggests that the quantum Fisher information matrix might be singular at the critical point, which in the context of parameter estimation is typically representing a significant complication. On the example of a toy-model Landau-Zener Hamiltonian, the Ising Hamiltonian, and the thermodynamic limit of the Lipkin-Meshkov-Glick Hamiltonian, we show that the quantum Fisher information matrix in critical metrology is always singular regardless of the system size and the distance to the critical point. However, contrary to the regular approach to metrology, where the singularity is detrimental, we argue that critical metrology works precisely because the quantum Fisher information matrix is singular.

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March 19, 2024
prof. dr hab. Piotr Szymczak
Faculty of Physics, University of Warsaw
"On the Ideal Shapes of Stalagmites"

Stalagmites are column-like formations that rise from the floor of caves. They are formed by the buildup of minerals deposited from water dripping from the ceiling. The water dissolves minerals, such as calcium carbonate, from the rock above. As the water drips down, it loses carbon dioxide to the cave air. This causes the minerals to come out of solution and precipitate onto the cave floor, slowly building up the stalagmite.

Nearly sixty years ago, Franke formulated a mathematical model for the growth of stalagmites. In this model, the local growth rate of a stalagmite is proportional to the oversaturation of calcium ions in the solution dripping down the stalagmite's surface. Franke postulated that - provided the physical conditions in the cave remain constant - after a sufficiently long period, the stalagmite will assume an ideal shape, which in later stages of growth will only move upwards without further change in its form. These conclusions were later confirmed in computer simulations yet the mathematical form of this ideal shape was not discovered.

As we will show, Franke's model for stalagmite growth can be solved analytically, finding invariant, Platonic forms of stalagmites that could be observed in an "ideal cave", under constant physical conditions and with a constant flow of water dripping from an associated stalactite. Interestingly, it turns out that the shape numerically found in previous numerical studies is just one of a whole family of solutions. These new solutions describe stalagmites with a flat area at their peak of a certain fixed diameter, and conical stalagmites, with sharply pointed tops. All of these forms are observed in caves.

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March 12, 2024
dr Helgi Sigurðsson
Faculty of Physics, University of Warsaw & Science Institute, University of Iceland
"Interacting Networks of Liquid Light"

Recent years have seen a surge of advancements in optical manipulation over bosonic light-matter quasiparticles known as exciton-polaritons in semiconductor microcavities. These particles appear under strong-coupling conditions between confined cavity photons and embedded quantum-well excitons. Characterised by very high interaction strengths, nonlinearities, and picosecond timescales, they provide an exciting testbed to explore room-temperature nonequilibrium Bose-Einstein condensation in the optical regime.

In this talk, I will present results on all-optically engineered macroscopic networks of connected exciton-polariton condensates, which permit studies on fundamental emergent behaviours in nonequilibrium quantum fluidic systems that are subject to an external drive and dissipation. I will explain how pumped polariton fluids give rise to so-called “ballistic condensates” which can interfere to form a bosonic analog of time-delay coupled oscillations, a behavior found all across nature. I will present experimental and theoretical results on large-scale condensate networks displaying aforementioned emergent behaviors, including: spontaneous synchronization with unprecedented long-range spatial and temporal correlations [1,2], formation of persistent circulating mass currents [3], non-invasive optical control of the network coupling weights [4], synthesis of artificial lattices for studies of non-Hermitian topological physics and Bloch band formation [5,6], and vortex frustration [7].

Lastly, I will discuss recent developments on the role of polariton condensate networks as nonlinear information processing elements in the optical computing paradigm. I will address three examples: room-temperature optical logic, analog spin simulators, and as neuromorphic computing hardware.

[1] Töpfer et al., Communication Physics 3, 2 (2020).
[2] Töpfer et al., Optica 8, 106 (2021).
[3] Cookson et al., Nature Communications 12, 2120 (2021).
[4] Alyatkin et al., Physical Review Letters 124, 207402 (2020).
[5] Pickup et al., Nature Communications 11, 4431 (2020).
[6] Alyatkin et al., Nature Communications 12, 5571 (2021).
[7] Alyatkin et al., arXiv:2207.01850 (2022).

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March 5, 2024
prof. Zbigniew R. Struzik
University of Tokyo
"On the dynamics of progress"

Autonomy is a unique defining feature of living systems, from bacteria -- or even from viruses, the organisms at the 'edge of life' -- striving to survive in evolving environment. Yet, evolution is a collective phenomenon requiring interaction, 'counterintuitively' to autonomic thinking of individual organisms allowing their species to survive.
Such an apparent dichotomy and the struggle of the 'opposites' is ubiquitous in most complex dynamical systems, entailing complex adaptive systems which encompass living systems. The struggle of the opposites underlies most if not all roads to progress, understood as the evolution of 'fitness' -- be it adaptation to environment for species survival or evolution of scientific paradigms, or indeed, the evolution of the market share for those financially challenged.

Curiously, the concept of the 'roads to progress' has to date not sufficiently been studied using the language of physics of complexity. Indeed, physics traditionally understood, stayed away from investigating phenomena involving engaging in any laws of -- and due to -- individual and individualised behaviour. Yet, as becomes apparent, such seemingly impenetrable problems as evolution of social standards such as morality or religion are not principally different from evolution of scientific paradigms and innovation, these in turn not being that different from the evolution of generic actors in a competitive company market.

Such universality is where physics can flourish and indeed, a rapidly growing range of reports shows intriguing beauty of the phenomena characterising the dynamics of the road to progress. In my talk, I will present our own recent work on the game-of-life like system which - to our surprise - showed exciting richness of critical phenomena. I will also refer to selected works in order to encourage listeners to engage in research of the 'physics of struggle'.

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February 20, 2024
dr Amir Rahmani Email View details
Institute of Physics PAS
"Non-Hermitian physics and phase transitions"

A physical system may become non-conservative when it is interacting with its environment. One way to introduce openness is by breaking the Hermiticity, that is, by involving non-Hermitian matrices/operators. This seminar will provide a quick overview of the theoretical background of non-Hermitian physics, followed by a focus on the topic of non-Hermitian phase transitions intertwined with the physics of light-matter interactions.

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February 13, 2024
prof. Gediminas Juzeliūnas
Institute of Theoretical Physics and Astronomy, Vilnius University, Vilnius, Lithuania
"Spin Squeezing for Ultracold Fermions in Optical Lattices"

In the initial part of the talk an extended overview will be presented on individual and collective spins, the states of the collective spin, squeezing the collective spin states. We will also talk about different spin squeezing mechanisms including one axis twisting (OAT), and two axis countertwisting (TACT) spin squeezing models. Subsequently we will discuss possibilities to produce spin squeezing for spinful atomic fermions in optical lattices. It is shown that by applying laser radiation one can simulate not only OAT but also TACT spin squeezing models, the latter TACT model providing better squeezing. The spin squeezing generated in this way is mediated by spin waves playing a role of the intermediate states facilitating the squeezing process. The spin squeezing can be used for increasing sensitivity of atomic clocks.

More about this work:
Phys. Rev. Lett. 129, 090403 (2022)
Phys. Rev. B 108, 104301 (2023)

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Liu Bin, Zhuorui Li, Lisen Bi, et al, incl. Panagiotis E. Theodorakis Email Website View details
Evaporation Dynamics of Deionized Water Droplets on Rough Substrates: The Coupling of Stick-Jump Motion and Evaporation
J. Heat Mass Transfer., 146(11), 111601 (2024)
#26 Number of Publications
I. Białynicki-Birula, Z. Białynicka-Birula Email View details , S. Augustynowicz
Reply to comments on 'Backflow in relativistic wave equations'
J. Phys. A: Math. Theor., 56, 138001 (2023)
T. Zeng, B. Liu, L. Bi, et al, incl. P. E. Theodorakis Email Website View details
Effects of different drying methods on quality and water distribution of Lycium barbarum
J. Food Process Eng., 46(12), e14482 (2023)
A. Eisenreichova , M. Klima , M. M. Anila, et al, incl. B. Różycki Email Website View details
Crystal Structure of the ORP8 Lipid Transport ORD Domain: Model of Lipid Transport
Cells, 12(15), 1974 (2023)
Xiaofang Shan, Bin Liu, Zongsheng Zhu, Rachid Bennacer, Rounan Wang, Panagiotis E. Theodorakis Email Website View details
Analysis of the heat transfer in electronic radiator filled with metal foam
Energies, 16, 4224 (2023)
Liu Bin, Hu Hengxiang, Bi Lisen, Panagiotis E. Theodorakis Email Website View details , Zeng Tao
Effect of the arrangement of two nozzles on morphology, velocity, and particle size distribution of artificial snow-making spray field
Physics of Fluids, 35, 052236 (2023)
Reinhard Lipowsky, Rikhia Ghosh, Vahid Satarifard, et al, incl. Bartosz Różycki Email Website View details
Leaflet Tensions Control the Spatio-Temporal Remodeling of Lipid Bilayers and Nanovesicles
Biomolecules, 13(6), 926 (2023)
Vu V. Q., Nissley D. A., Jiang Y., O’Brien E. P., Li M. S. Email Website View details
Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study
J. Phys. Chem. B, 127 (21), 4761 (2023)
Gabovich A. M., Voitenko A. I., Ekino T., et al, incl. Li M. S. Email Website View details
Coexistence of superconductivity and charge-density waves: evidence from tunneling studies
Low Temperature Physics, 49(7), 881 (2023)
N. Karska, I. Zhukov, A. D. Lipińska, S. Rodziewicz-Motowidło, P. Krupa Email View details
Why does the herpes simplex 1 virus-encoded UL49.5 protein fail to inhibit the TAP-dependent antigen presentation?
BBA-Biomembranes, 1865(8), 184200 (2023)
M. Graul, N. Karska, M. Wąchalska, et al, incl. P. Krupa Email View details
The N-terminal Proline Hinge Motif Controls the Structure of Bovine Herpesvirus 1-encoded Inhibitor of the Transporter Associated with Antigen Processing Required for its Immunomodulatory Function
Journal of Molecular Biology, 435, 167964 (2023)
L. Bi, B. Liu, Z. Zhu, P. E. Theodorakis Email Website View details , H. Hu,  Z. Li 
Molecular dynamics simulation of Wenzel-state nanodroplets: Evaporation on heated substrates with different rough structures
Physics of Fluids, 35, 012015 (2023)
B. Liu, Z. Li, L. Bi, et al, incl. P. E. Theodorakis Email Website View details
Characteristics of HFE7100 droplets evaporation on substrates with different thermal conductivity
Thermal Science and Engineering Progress, 40, 101771 (2023)
#57 Number of Publications
A. Chen, H. Zhang, J. Song, B. Liu, C. Zhang, P. E. Theodorakis Email Website View details
On the meniscus shape and marangoni flow in capillary tubes with noncircular cross-section shapes
Eur. Phys. J. Appl. Phys. , 97, 77 (2022)
N. H. Linh, V. H. Man, M. S. Li Email Website View details , et al
Molecular dynamics simulation of cancer cell membrane perforated by shockwave induced bubble collapse
J. Chem. Phys., 157, 225102 (2022)
B.A. Orlowski , K. Gwozdz, K. Goscinski, et al
Extended Defect States in CdTe/ZnTe Photojunction
Acta Phys. Pol. , 5, 548 (2022)
H. Nguyen, M. S. Li Email Website View details
Antibody–nanobody combination increases their neutralizing activity against SARS-CoV-2 and nanobody H11-H4 is effective against Alpha, Kappa and Delta variants
Scientific Reports, 12, 9701 (2022)
H. L. Nguyen, N. Q. Thai, P. H. Nguyen, M. S. Li Email Website View details
SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation
J. Phys. Chem. B, 126, 4669 (2022)
H. L. Nguyen, N. Q. Thai, M. S. Li Email Website View details
Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution
J. Chem. Theory Comput., 18, 3860 (2022)
J. Dorival, S. Moraïs, A. Labourel, et al
Mapping the deformability of natural and designed cellulosomes in solution
Biotechnology for Biofuels and Bioproducts, 15, 68 (2022)
H. L. Nguyen, V. H. Man, M. S. Li Email Website View details , P. Derreumaux, J. Wang,  P. H. Nguyen
Elastic moduli of normal and cancer cell membranes revealed by molecular dynamics simulations
Phys. Chem. Chem. Phys., 24, 6225 (2022)
H. Nguyen, P. D. Lan, D. A. Nissley, E. P. O’Brien, M. S. Li Email Website View details
Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability
J. Phys. Chem. B, 126, 2812 (2022)
A. Liwo, A. K. Sieradzan, A. S. Karczyńska, et al, incl. P. Krupa Email View details
Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
Practical Aspects of Computational Chemistry, V, 31 (2022)
#49 Number of Publications
P. Comaron, I. Carusotto, M. H. Szymańska, N. P. Proukakis
Non-equilibrium Berezinskii-Kosterlitz-Thouless transition in driven-dissipative condensates
Europhysics Letters , 133, 17002 (2021)
A. K. Sieradzan, C. Czaplewski, P. Krupa Email View details , et al
Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
Protein Folding, Methods in Molecular Biology , 2376, 399 (2021)
A. Antoniak, I. Biskupek, K.  K.Bojarski, et al, incl. P. Krupa Email View details
Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
Journal of Molecular Graphics and Modelling , 108, 108008 (2021)
M. Król, K. Rechcińska, H. Sigurdsson, et al, incl. M. Matuszewski Email Website View details
Realizing Optical Persistent Spin Helix and Stern-Gerlach Deflection in an Anisotropic Liquid Crystal Microcavity
Physical Review Letters , 127, 190401 (2021)
A. M. Vera, A. Galera-Prat, M. Wojciechowski, et al, incl. B. Różycki Email Website View details
Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization
Structure, 29, 587 (2021)
Q. V. Vu, Y. Jiang, M. S. Li Email Website View details , E. P. O'Brien
The Driving Force for Co-translational Protein Folding is Weaker In the Ribosome Vestibule due to Greater Water Ordering
Chemical Science , 12, 11851 (2021)
A. Eisenreichova, B. Różycki Email Website View details , E. Boura, J. Humpolickova
Osh6 Revisited: Control of PS Transport by the Concerted Actions of PI4P and Sac1 Phosphatase
Frontiers in Molecular Bioscience, 8, 747601 (2021)
V. H. Man, M. S. Li Email Website View details , P. Derreumaux, J. Wang, P. H. Nguyen
Molecular Mechanism of Ultrasound-Induced Structural Defects in Liposomes: A Nonequilibrium Molecular Dynamics Simulation Study
Langmuir, 37, 7945 (2021)
H. Nguyen, P. D. Lan, D. A. Nissley, E. P. O’Brien, M. S. Li Email Website View details
Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody
J. Phys. Chem. B, 125, 7368 (2021)
A. B. Poma, T. T. M. Thu, L. T. M. Tri, H. L. Nguyen, M. S. Li Email Website View details
Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations
J. Phys. Chem. B, 125, 7628 (2021)
R. Szymko, M. Denys, T. Bulik, et al
Application of Spatio-Temporal Spectral Analysis for Detection of SeismicWaves in Gravitational-Wave Interferometer
Galaxies, 9, 50 (2021)
P. Krupa Email View details , A. S. Karczyńska, M. A. Mozolewska, A. Liwo, C. Czaplewski
UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
Bioinformatics , 37, 1613 (2021)
P. Krupa Email View details , M. Spodzieja, A. K.Sieradzan
Prediction of CD28-CD86 protein complex structure using different level of resolution approach
Journal of Molecular Graphics and Modelling, 103, 107802 (2021)
D. Marasco, C. Vicidomini, P. Krupa Email View details , et al, incl. M. S. Li Email Website View details
Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine-based compounds on β-amyloid aggregation
Chemico-Biological Interactions, 334, 109300 (2021)
P. E. Theodorakis Email Website View details , Y. Wang, A. Chen, B. Liu
Off-lattice Monte-Carlo approach for studying nucleation and evaporation phenomena at the molecular scale
Materials, 14, 2092 (2021)
R. Rechciński, M. Galicka, M. Simma, et al, incl. P. Kacman , R. Buczko Email Website View details
Structure Inversion Asymmetry and Rashba Effect in Quantum Confined Topological Crystalline Insulator Heterostructures
Adv. Funct. Mater., 31, 2008885 (2021)
M. Banchelli, R. Cascella, C. D’Andrea, et al, incl. M. S. Li Email Website View details
Probing the Structure of Toxic Amyloid-β Oligomers with Electron Spin Resonance and Molecular Modeling
ACS Chemical Neuroscience, 12, 1150 (2021)
L. Li, J. Hu, X. Shi, B. Różycki Email Website View details , F. Song
Interplay between cooperativity of intercellular receptor-ligand binding and coalescence of nanoscale lipid clusters in adhering membranes
Soft Matter, 17, 1912 (2021)
K. Brown, T. Bland, P. Comaron, N. P. Proukakis
Periodic quenches across the Berezinskii-Kosterlitz-Thouless phase transition
Phys. Rev. Research, 3, 013097 (2021)
P. H. Nguyen, A. Ramamoorthy, B. R. Sahoo, et al, incl. M. S. Li Email Website View details
Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
Chem. Rev., 121, 2545 (2021)
#61 Number of Publications
A. S. Karczynska, K. Zieba, U. Uciechowska, et al, incl. P. Krupa Email View details
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
Journal of Chemical Information and Modeling, 60, 1844 (2020)
A. Liwo, C. Czaplewski, A. K. Sieradzan, et al, incl. P. Krupa Email View details
Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
Progress in Molecular Biology and Translational Science, 170, 73 (2020)
D. A. Nissley, Q. V. Vu, F. Trovato, et al, incl. M. S. Li Email Website View details
Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling
Journal of the American Chemical Society, 142, 6103 (2020)
H. L. Nguyen, T. Q. Nguyen, D, T. Truong, M. S. Li Email Website View details
Remdesivir Strongly Binds to both RNA-dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations
The Journal of Physical Chemistry B, 124, 11337 (2020)
H. L. Nguyen, L. D. Pham, T. Q. Nguyen, D. A. Nissley, E. P. O’Brien, M. S. Li Email Website View details
Does SARS-CoV-2 Bind to Human ACE2 More Strongly Than Does SARS-CoV?
The Journal of Physical Chemistry B, 124, 7336 (2020)
A. M. Gabovich, M. S. Li Email Website View details , H. Szymczak, A. I. Voitenko 
Electric dipole image forces in three-layersystems: The classical electrostatic model
The Journal of Chemical Physics, 152, 094705 (2020)
T. C. Nguyen, L. D. Pham, D. Q. H. Pham, M. S. Li Email Website View details
Heat-induced degradation of fibrils: Exponential vs logistic kinetics
The Journal of Chemical Physics, 152, 115101 (2020)
M. Gancar, K. Ho, Sk. A. Mohid, et al, incl. M. S. Li Email Website View details
7 Methoxytacrine and 2 Aminobenzothiazole Heterodimers: Structure−Mechanism Relationship of Amyloid Inhibitors Based on Rational Design
ACS Chemical Neuroscience, 11, 715 (2020)
T. Q. Nguyen, P. E. Theodorakis Email Website View details , M. S. Li 
Fast estimation of the blood-brain barrier permeability by pulling a ligand through a lipid membrane
Journal of Chemical Information and Modeling, 60, 3057 (2020)
S. Boopathi,  D. Q. H. Pham,  W. Gonzalez, P. E. Theodorakis Email Website View details , M. S. Li Email Website View details
Zinc binding promotes greater hydrophobicity in Alzheimer’s Ab42 peptide than copper binding: Molecular dynamics and solvation thermodynamics studies
Proteins: Structure, function and bioinformatics, 88, 1285 (2020)
M. Banchelli, R. Cascella, C. D'Andrea, et al, incl. M. S. Li Email Website View details
Nanoscopic insights into the surface conformation of neurotoxic amyloid β oligomers
The Royal Society of Chemistry Advances, 10, 21907 (2020)
H. L. Nguyen, L. D. Pham, T. Q. Nguyen, D. A. Nissley, E. P. O’Brien, M. S. Li Email Website View details
Does SARS-CoV 2 Bind to Human ACE2 More Strongly Than Does SARS-CoV?
The Journal of Physical Chemistry B, 124, 7336 (2020)
V. M. Hoang, M. S. Li Email Website View details , P. Derreumaux, et al
Molecular mechanism of ultrasound interaction with a blood brain barrier model
The Journal of Chemical Physics, 153, 045104 (2020)
T. Ekino, A. M. Gabovich, M. S. Li Email Website View details , H. Szymczak, A. I. Voitenko 
Break-junction tunneling spectra of Bi2212 superconducting ceramics: Influence of inhomogeneous d-wave-Cooper-pairing and charge-density-wave order parameters
Low Temperature Physics, 46, 400 (2020)
B. Liu, S.W. Wang, L. Chai, G. El Achkar, A. Chen, P. E. Theodorakis Email Website View details
Experimental investigation of nanoparticles distribution mechanisms and deposition patterns during nanofluid droplet evaporation
Eur. Phys. J. Appl. Phys., 92, 11101 (2020)
A. Zamora, G. Dagvadorj, P. Comaron, I. Carusotto, N. P. Proukakis, M. H. Szymańska
Kibble-Zurek Mechanism in Driven Dissipative Systems Crossing a Nonequilibrium Phase Transition
Phys. Rev. Lett., 125, 095301 (2020)
V. Shahnazaryan, V. K. Kozin, I. A. Shelykh, I. V. Iorsh, and O. Kyriienko
Tunable optical nonlinearity for transition metal dichalcogenide polaritons dressed by a Fermi sea
Phys. Rev. B, 102, 115310 (2020)
R. Jakieła, M. Galicka, P. Dziawa, G. Springholz, A. Barcz
SIMS accurate determination of matrix composition of topological crystalline insulator material Pb1-xSnxSe
Surface and Interface Analysis, 52, 71 (2020)
T. Bland, Q. Marolleau, P. Comaron, B. A. Malomed, N. P. Proukakis
Persistent current formation in double-ring geometries
J. Phys. B: Al. Mol. Opt. Phys., 52, 115301 (2020)
#62 Number of Publications