Scientific publications
2022
- R. Mirek, A. Opala, M. Furman, M. Król, K. Tyszka, B. Seredyński, W. Pacuski, J. Suffczyński, J. Szczytko, M. Matuszewski, B. Piętka
Neural Networks Based on Ultrafast Time-Delayed Effects in Exciton Polaritons
Phys. Rev. Applied 17, 054037 (2022) DOI: 10.1103/PhysRevApplied.17.054037, ArXiv: 2201.00225
- H. Nguyen, M. S. Li
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) DOI: 10.1038/s41598-022-14263-1
- H. L. Nguyen, N. Q. Thai, P. H. Nguyen, M. S. Li
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) DOI: 10.1021/acs.jpcb.2c01048
- M. Pylak, F. Gampel, M. Płodzień, M. Gajda
Manifestation of relative phase in dynamics of two interacting Bose-Bose droplets
Phys. Rev. Research 4, 013168 (2022) DOI: 10.1103/PhysRevResearch.4.013168, ArXiv: 2104.06895
- H. L. Nguyen, N. Q. Thai, M. S. Li
Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution
J. Chem. Theory Comput. 18, 3860 (2022) DOI: 10.1021/acs.jctc.1c01158
- I. Bialynicki-Birula, Z. Bialynicka-Birula, S. Augustynowicz
Backflow in relativistic wave equations
J. Phys. A: Math. Theor. 55, 255702 (2022) DOI: 10.1088/1751-8121/ac65c1, ArXiv: 2204.10880
- B. Różycki, E. Boura
Conformational ensemble of the full-length SARS-CoV-2 nucleocapsid (N) protein based on molecular simulations and SAXS data
Biophysical Chemistry 288, 106843 (2022) DOI: 10.1016/j.bpc.2022.106843
- J. Dorival, S. Moraïs, A. Labourel, B. Rozycki, P.-A. Cazade, J. Dabin, E. Setter-Lamed, I. Mizrahi, D. Thompson, A. Thureau, E. A. Bayer, M. Czjzek
Mapping the deformability of natural and designed cellulosomes in solution
Biotechnology for Biofuels and Bioproducts 15, 68 (2022) DOI: 10.1186/s13068-022-02165-3
- B. Liu, S. Shi, H. Yin, P. E. Theodorakis, R. Bennacer
COMPARATIVE EXPERIMENTAL STUDY ON MICROCHANNEL AND FINNED-TUBE EVAPORATORS IN A WINDOW AIR-CONDITIONING SYSTEM
Journal of Enhanced Heat Transfer 29, 51 (2022) DOI: 10.1615/JEnhHeatTransf.2022042367
- I. Bialynicki-Birula, Z. Bialynicka-Birula
Ehrenfest theorem in relativistic quantum theory
J. Phys. B: At. Mol. Opt. Phys 55, 114001 (2022) DOI: 10.1088/1361-6455/ac65c6, ArXiv: 2111.10798
- H. L. Nguyen, H. Q. Linh, P. Krupa, G. La Penna, M. S. Li
Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity
J. Phys. Chem. B 126, 3659 (2022) DOI: 10.1021/acs.jpcb.2c01769
- P. Szulim, M. Trippenbach, Y. B. Band, M. Gajda, M. Brewczyk
Atoms in a spin dependent optical potential: ground state topology and magnetization
New J. Phys. 24, 033041 (2022) DOI: 10.1088/1367-2630/ac59ed
- M. Pylak, F. Gampel, M. Płodzień, M. Gajda
Manifestation of relative phase in dynamics of two interacting Bose-Bose droplets
Phys. Rev. Research 4, 013168 (2022) DOI: 10.1103/PhysRevResearch.4.013168
- A. M. Gabovich , M. S. Li, H. Szymczak , A. I. Voitenko
Charge-charge interaction in three-layer systems: Classical approach
Phys.Rev. B 105, 115415 (2022) DOI: 10.1103/PhysRevB.105.115415
- H. L. Nguyen, V. H. Man, M. S. Li, 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) DOI: 10.1039/d1cp04836h
- H. Nguyen, P. D. Lan, D. A. Nissley, E. P. O’Brien, M. S. Li
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) DOI: 10.1021/acs.jpcb.2c00708
- Z. Zeng, T. Wang, R. Chen, M. Suo, K. Sun, P. E. Theodorakis, Z. Che
Two-dimensional partitioned square ice confined in graphene/graphite nanocapillaries
J. Chem. Phys. 156, 154510 (2022) DOI: 10.1063/5.0087690, ArXiv: 2204.03198
- P. E. Theodorakis, S. A. Egorov, A. Milchev
Rugotaxis: Droplet motion without external energy supply
EPL 137, 43002 (2022) DOI: 10.1209/0295-5075/ac55f2
- I. Białynicki-Birula, Z. Białynicka-Birula
Comment on "Possibility of small electron states"
Phys.Rev. A 105, 036201 (2022) DOI: 10.1103/PhysRevA.105.036201, ArXiv: 2105.07726
- N. T. Co, M. S. Li, P. Krupa
Computational Models for the Study of Protein Aggregation
Computer Simulations of Aggregation of Proteins and Peptides, Methods in Molecular Biology 2340, 51 (2022) DOI: 10.1007/978-1-0716-1546-1_4
- A. J. Groszek, P. Comaron, N. P. Proukakis, T. P. Billam
Crossover in the dynamical critical exponent of a quenched two-dimensional Bose gas
Phys. Rev. Research 3, 013212 (2021) DOI: 10.1103/PhysRevResearch.3.013212, ArXiv: 2006.13284
- 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) DOI: 10.1209/0295-5075/133/17002, ArXiv: 2011.06365
- B. Liu, J. Li, A. Chen, P. E. Theodorakis, Z. Zhu, J. Yu
Selection of the cold logistics model based on the carbon footprint of fruits and vegetables in China
Journal of Cleaner Production 334, 130251 (2022) DOI: 10.1016/j.jclepro.2021.130251
- S. Zhao, X. Han, B. Liu, S. Wang, W. Guan, Z. Wu, P. E. Theodorakis
Shelf-life prediction model of fresh-cut potato at different storage temperatures
Journal of Food Engineering 317, 110867 (2022) DOI: 10.1016/j.jfoodeng.2021.110867
- B. Liu, S. Shi, Y. Liu, R. Bennacer, A. Chen, P. E. Theodorakis
Effect of Different Plenum-Chamber Coefficients on the Frosting of Air-Cooler
Energies 15, 422 (2022) DOI: 10.3390/en15020422
- F. Gampel, M. Gajda, M. Załuska–Kotur, J. Mostowski
Pauli crystals in harmonic trap and on a sphere
Physics Letters A 422, 127799 (2022) DOI: 10.1016/j.physleta.2021.127799, ArXiv: 2105.13914
- G. Ramon, Ł. Cywiński
Qubit decoherence under two-axis coupling to low-frequency noises
Phys. Rev. B 105, L041303 (2022) DOI: 10.1103/PhysRevB.105.L041303, ArXiv: 2112.03438
- A. Liwo, A. K. Sieradzan, A. S. Karczyńska, E. A. Lubecka, S. A. Samsonov, C. Czaplewski, P. Krupa, M. Mozolewska
Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
Practical Aspects of Computational Chemistry V, 31 (2022) DOI: 10.1007/978-3-030-83244-5_2
2021
- S. E. Leininger, J. Rodriguez, Q. V. Vu, Y. Jiang, M. S. Li, C. Deutsch, E. P. O’Brien
Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force
Biochemistry 60, 3223 (2021) DOI: 10.1021/acs.biochem.1c00507
- D. Włodzyński, T. Sowiński
Few strongly interacting fermions of different mass driven in the vicinity of a critical point
Phys. Rev. A 104, 053317 (2021) DOI: 10.1103/PhysRevA.104.053317, ArXiv: 2103.01798
- J. Dobrzyniecki, G. Orso, T. Sowiński
Unconventional pairing in few-fermion systems tuned by external confinement
Phys. Rev. Research 3, 043105 (2021) DOI: 10.1103/PhysRevResearch.3.043105, ArXiv: 2105.12519
- A. K. Sieradzan, C. Czaplewski, P. Krupa, M. A. Mozolewska, A. S. Karczyńska, A. G. Lipska, E. A. Lubecka, E. Gołaś, T. Wirecki, M. Makowski, S. Ołdziej, A. Liwo
Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
Protein Folding, Methods in Molecular Biology 2376, 399 (2021) DOI: 10.1007/978-1-0716-1716-8_23
- A. Antoniak, I. Biskupek, K. K.Bojarski, C. Czaplewski, A. Giełdoń, M. Kogut, M. M.Kogut, P. Krupa, A. G.Lipska, A. Liwo, E. A.Lubecka, M. Marcisz, M. Maszota-Zieleniak, S. A.Samsonov, A. K.Sieradzan, M. J.Ślusarz, R. Ślusarz, P. A.Wesołowski, K. Ziȩba
Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
Journal of Molecular Graphics and Modelling 108, 108008 (2021) DOI: 10.1016/j.jmgm.2021.108008
- G. Dagvadorj, M. Kulczykowski, M. H. Szymańska, M. Matuszewski
First-order dissipative phase transition in an exciton-polariton condensate
Physical Review B 104, 165301 (2021) DOI: 10.1103/PhysRevB.104.165301, ArXiv: 2104.07385
- M. Król, K. Rechcińska, H. Sigurdsson, P. Oliwa, R. Mazur, P. Morawiak, W. Piecek, P. Kula, P. G. Lagoudakis, M. Matuszewski, W. Bardyszewski, B. Piętka, J. Szczytko
Realizing Optical Persistent Spin Helix and Stern-Gerlach Deflection in an Anisotropic Liquid Crystal Microcavity
Physical Review Letters 127, 190401 (2021) DOI: 10.1103/PhysRevLett.127.190401
- M. S. Song, T. Koren, M. Załuska-Kotur, R. Buczko, N. Avraham, P. Kacman, H. Shtrikman, H. Beidenkopf
Sub-Band Spectrum Engineering via Structural Order in Tapered Nanowires
Nano Lett. 21, 10215 (2021) DOI: 10.1021/acs.nanolett.1c03071
- B. Liu, S. Shi, Y. Liu, R. Bennacer, A. Chen, P. E. Theodorakis
Study on the effect of different plenum chamber coefficients on frosting of air-cooler
E3S Web Conferences 321, 04019 (2021) DOI: 10.1051/e3sconf/202132104019
- A. M. Vera, A. Galera-Prat, M. Wojciechowski, B. Różycki, D. V. Laurents, M. Carrión-Vázquez, M. Cieplak, P. Tinnefeld
Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization
Structure 29, 587 (2021) DOI: 10.1016/j.str.2021.01.006
- Q. V. Vu, Y. Jiang, M. S. Li, 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) DOI: 10.1039/D1SC01008E
- A. Eisenreichova, B. Różycki, 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) DOI: 10.3389/fmolb.2021.747601
- P. R. Pandey, B. Różycki, R. Lipowsky, T. R. Weikl
Structural variability and concerted motions of the T cell receptor – CD3 complex
eLife 10, e67195 (2021) DOI: 10.7554/eLife.67195
- M. Załuska-Kotur , H. Popova, V. Tonchev
Step Bunches, Nanowires and Other Vicinal "Creatures"—Ehrlich–Schwoebel Effect by Cellular Automata
Crystals 11, 1135 (2021) DOI: 10.3390/cryst11091135
- P. Szańkowski
Measuring trajectories of environmental noise
Phys. Rev. A 104, 022202 (2021) DOI: 10.1103/PhysRevA.104.022202, ArXiv: 2106.08434
- I. Białynicki-Birula, Z. Białynicka-Birula
Time crystals made of electron-positron pairs
Phys. Rev. A 104, 022203 (2021) DOI: 10.1103/PhysRevA.104.022203, ArXiv: 2105.04346
- J. A. Krzywda, Ł. Cywiński
Interplay of charge noise and coupling to phonons in adiabatic electrontransfer between quantum dots
Phys. Rev. B 104, 075439 (2021) DOI: 10.1103/PhysRevB.104.075439, ArXiv: 2104.07581
- M. Matuszewski , A. Opala, R. Mirek , M. Furman, M. Król , K. Tyszka , T.C.H. Liew, D. Ballarini, D. Sanvitto, J. Szczytko, B. Piętka
Energy-Efficient Neural Network Inference with Microcavity Exciton Polaritons
Phys. Rev. Applied 16, 024045 (2021) DOI: 10.1103/PhysRevApplied.16.024045, ArXiv: 2108.12648
- H. A. Pham, D. T. Truong, M. S. Li
Dependence of Work on the Pulling Speed in Mechanical Ligand Unbinding
J. Phys. Chem. B 125, 8325 (2021) DOI: 10.1021/acs.jpcb.1c01818
- S. Ghosh , A. Opala, M. Matuszewski , T. Paterek , T. C. H. Liew
Reconstructing Quantum States With Quantum Reservoir Networks
IEEE Trans. Neural Netw. Learn. Syst. 32, 3148 (2021) DOI: 10.1109/TNNLS.2020.3009716, ArXiv: 2008.06378
- T. Sowiński
Few-body perspective on fermionic pairing in one spatial Dimension
Europhys. Lett. 134, 33001 (2021) DOI: 10.1209/0295-5075, ArXiv: 2105.13030
- V. H. Man, M. S. Li, 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) DOI: 10.1021/acs.langmuir.1c00555
- H. Nguyen, P. D. Lan, D. A. Nissley, E. P. O’Brien, M. S. Li
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) DOI: 10.1021/acs.jpcb.1c03639
- A. B. Poma, T. T. M. Thu, L. T. M. Tri, H. L. Nguyen, M. S. Li
Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations
J. Phys. Chem. B 125, 7628 (2021) DOI: 10.1021/acs.jpcb.1c02322
- R. Szymko , M. Denys, T. Bulik , B. Idźkowski, A. Kutynia, K. Nikliborc, M. Suchiński
Application of Spatio-Temporal Spectral Analysis for Detection of SeismicWaves in Gravitational-Wave Interferometer
Galaxies 9, 50 (2021) DOI: 10.3390/galaxies9030050, ArXiv: 2102.04244
- P. Kościk, A. Kuroś, A. Pieprzycki, T. Sowiński
Pair-correlation ansatz for the ground state of interacting bosons in an arbitrary one-dimensional potential
Sci. Rep. 103, 045202 (2021) DOI: 10.1038/s41598-021-92556-7, ArXiv: 2104.07953
- P. Krupa, 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) DOI: 10.1093/bioinformatics/btaa897
- R. Mirek, A. Opala, P. Comaron, M. Furman, M. Król, K. Tyszka, B. Seredyński, D. Ballarini, D. Sanvitto, T. C. H. Liew, W. Pacuski, J. Suffczyński, J. Szczytko, M. Matuszewski, B. Piętka
Neuromorphic Binarized Polariton Networks
Nano Lett. 21, 3715 (2021) DOI: 10.1021/acs.nanolett.0c04696
- P. Krupa, 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) DOI: 10.1016/j.jmgm.2020.107802
- D. Marasco, C. Vicidomini, P. Krupa , F. Cioffi , P. D. Q. Huy , M. S. Li , D. Florio, K. Broersen, M. F. De Pandis, G. N. Roviello
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) DOI: 10.1016/j.cbi.2020.109300
- P. E. Theodorakis, A. Amirfazli, B. Hu, Z. Che
Droplet control based on pinning and substrate wettability
Langmuir 37, 4248 (2021) DOI: 10.1021/acs.langmuir.1c00215
- S. S. Mirkhalaf, D. B. Orenes, M. W. Mitchell, E. Witkowska
Criticality-enhanced quantum sensing in ferromagnetic Bose-Einstein condensates: Role of readout measurement and detection noise
Phys. Rev. A 103, 023317 (2021) DOI: 10.1103/PhysRevA.103.023317, ArXiv: 2010.13133
- P. E. Theodorakis, 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) DOI: 10.3390/ma14092092
- J. Pietraszewicz, A. Seweryn, E. Witkowska
Multifaceted phase ordering kinetics of an antiferromagnetic spin-1 condensate”
Sci. Rep. 11, 9296 (2021) DOI: 10.1038/s41598-021-88454-7, ArXiv: 1905.00662
- P. Deuar
Multi-time correlations in the positive-P, Q, and doubled phase-space representations
Quantum 5, 455 (2021) DOI: 10.22331/q-2021-05-10-455, ArXiv: 2011.10107
- M. Denys
Model of cunning agents
Physica A 574, 125987 (2021) DOI: 10.1016/j.physa.2021.125987, ArXiv: 2012.08517
- M. B. Christensen, T. Vibel, A. J. Hilliard, M. B. Kruk, K. Pawłowski, D. Hryniuk, K. Rzążewski, M. A. Kristensen, J. J. Arlt
Observation of Microcanonical Atom Number Fluctuations in a Bose-Einstein Condensate
Phys. Rev. Lett. 126, 153601 (2021) DOI: 10.1103/PhysRevLett.126.153601, ArXiv: 2011.08736
- L. Li, J. Hu, B. Różycki, X. Wang, H. Wu, F. Song
Influence of lipid rafts on pattern formation during T-cell adhesion
New J. Phys. 23, 043052 (2021) DOI: 10.1088/1367-2630/abeacb
- B. Różycki, T. R. Weikl
Cooperative stabilization of close-contact zones leads to sensitivity and selectivity in T-cell recognition
Cells 10, 1023 (2021) DOI: 10.3390/cells10051023
- R. Rechciński, M. Galicka, M. Simma, V. V. Volobuev, O. Caha, J. Sánchez-Barriga, P. S. Mandal, E. Golias, A. Varykhalov, O. Rader, G. Bauer, P. Kacman, R. Buczko, G. Springholz
Structure Inversion Asymmetry and Rashba Effect in Quantum Confined Topological Crystalline Insulator Heterostructures
Adv. Funct. Mater. 31, 2008885 (2021) DOI: 10.1002/adfm.202008885
- N.T. Co, M. S. Li
Effect of Surface Roughness on Aggregation of Polypeptide Chains: A Monte Carlo Study
Biomolecules 11, 596 (2021) DOI: 10.3390/biom11040596
- D. Kwiatkowski, Ł. Cywiński, J. K. Korbicz
Appearance of objectivity for NV centers interacting with dynamically polarized nuclear environment
New J. Phys. 23, 043036 (2021) DOI: 10.1088/1367-2630/abeffd, ArXiv: 2012.02855
- M. Banchelli, R. Cascella, C. D’Andrea, G. La Penna, M. S. Li, F. Machetti, P. Matteini, S. Pizzanelli
Probing the Structure of Toxic Amyloid-β Oligomers with Electron Spin Resonance and Molecular Modeling
ACS Chemical Neuroscience 12, 1150 (2021) DOI: 10.1021/acschemneuro.0c00714
- D. Nandy, T. Sowiński
Dynamical resistivity of a few interacting fermions to the time-dependent potential barrier
New J. Phys. 23, 043019 (2021) DOI: 10.1088/1367-2630/abee41, ArXiv: 2101.00892
- P. Zin, M. Pylak, M. Gajda
Zero-energy modes of two-component Bose–Bose droplets
New J. Phys. 23, 033022 (2021) DOI: 10.1088/1367-2630/abe482, ArXiv: 2011.05135
- T. Świsłocki, M. Gajda, M. Brewczyk, P. Deuar
Spin distillation cooling of ultracold Bose gases
Scientific Reports 11, 6441 (2021) DOI: 10.1038/s41598-021-85298-z, ArXiv: 2011.03507
- K. Roszak, Ł. Cywiński
Qubit-environment-entanglement generation and the spin echo
Phys. Rev. A 103, 032208 (2021) DOI: 10.1103/PhysRevA.103.032208, ArXiv: 2007.02656
- L. Li, J. Hu, X. Shi, B. Różycki, F. Song
Interplay between cooperativity of intercellular receptor-ligand binding and coalescence of nanoscale lipid clusters in adhering membranes
Soft Matter 17, 1912 (2021) DOI: 10.1039/D0SM01904F
- D. M. Irber, F. Poggiali, F. Kong, M. Kieschnick, T. Lühmann, D. Kwiatkowski, J. Meijer, J. Du, F. Shi, F. Reinhard
Robust all-optical single-shot readout of nitrogen-vacancy centers in diamond
Nature Communictions 12, 532 (2021) DOI: 10.1038/s41467-020-20755-3, ArXiv: 1909.11397
- M. Król, H. Sigurdsson, K. Rechcińska, P. Oliwa, K. Tyszka, W. Bardyszewski, A. Opala, M. Matuszewski, P. Morawiak, R. Mazur, W. Piecek, P. Kula, P. G. Lagoudakis, B. Piętka, J. Szczytko
Observation of second-order meron polarization textures in optical microcavities
Optica 8, 255 (2021) DOI: 10.1103/10.1364/OPTICA.414891, ArXiv: 2010.01691
- A. Łusakowski, P. Bogusławski, T. Story
Band structure and topological phases of (Pb,Sn,Mn)Te by first principles calculations
Phys. Rev. B 103, 045202 (2021) DOI: 10.1103/PhysRevB.103.045202, ArXiv: 2010.00874
- A. Ciechan, P. Bogusławski
Theory of the sp-d coupling of transition metal impurities with free carriers in ZnO
Sci. Rep. 11, 3848 (2021) DOI: 10.1038/s41598-021-83258-1, ArXiv: 2102.12338
- K. Brown, T. Bland, P. Comaron, N. P. Proukakis
Periodic quenches across the Berezinskii-Kosterlitz-Thouless phase transition
Phys. Rev. Research 3, 013097 (2021) DOI: 10.1103/PhysRevResearch.3.013097
- P. H. Nguyen, A. Ramamoorthy, B. R. Sahoo, J. Zheng, P. Faller, J. E. Straub, L. Dominguez, J.-E. Shea, N. V. Dokholyan, A. De Simone, B. Ma, R. Nussinov, S. Najafi, S. T. Ngo, A. Loquet, M. Chiricotto, P. Ganguly, J. McCarty, M. S. Li, C. Hall, Y. Wang, Y. Miller, S. Melchionna, B. Habenstein, S. Timr, J. Chen, B. Hnath, B. Strodel, R. Kayed, S. Lesné, G. Wei, F. Sterpone, A. J. Doig, and P. Derreumaux
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) DOI: 10.1021/acs.chemrev.0c01122
- P. Deuar, A. Ferrier, M. Matuszewski, G. Orso, M. H. Szymańska
Fully quantum scalable description of driven-dissipative lattice models
PRX Quantum 2, 010319 (2021) DOI: 10.1103/PRXQuantum.2.010319, ArXiv: 2012.02014
- T. Karpiuk, M. Nikołajuk, M. Gajda, M. Brewczyk
Modelling quantum aspects of disruption of a white dwarf star by a black hole
Sci. Rep. 11, 2286 (2021) DOI: 10.1038/s41598-021-81707-5, ArXiv: 1907.12419
- P. Zin, M. Pylak, M. Gajda
Revisiting a stability problem of two-component droplets
Phys. Rev. A 103, 013312 (2021) DOI: 10.1103/PhysRevA.103.013312, ArXiv: 2007.11817
- A. Sicorello, B. Różycki, P. V. Konarev, D. I. Svergun, A. Pastore
Capturing the conformational ensemble of the mixed folded polyglutamine protein ataxin-3
Structure 29, 70 (2021) DOI: 10.1016/j.str.2020.09.010
- J. Dobrzyniecki, T. Sowiński
Two Rydberg-dressed atoms escaping from an open well
Phys. Rev. A 103, 013304 (2021) DOI: 10.1103/PhysRevA.103.013304, ArXiv: 2009.04839
2020
- A. S. Karczynska, K. Zieba, U. Uciechowska, M. A. Mozolewska, P. Krupa, E. A. Lubecka, A. G. Lipska, C. Sikorska, S. A. Samsonov, A. K. Sieradzan, A. Giełdon, A. Liwo, R. Slusarz, M. Slusarz, J. Lee, K. Joo, C. Czaplewski
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) DOI: 10.1021/acs.jcim.9b00864
- A. Liwo, C. Czaplewski, A. K. Sieradzan, E. A. Lubecka, A. G. Lipska, Ł. Golon, A. Karczyńska, P. Krupa, M. A. Mozolewska, M. Makowski, R. Ganzynkowicz, A. Giełdoń, M. Maciejczyk
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) DOI: 10.1016/bs.pmbts.2019.12.004
- D. Ballarini, A. Gianfrate, R. Panico, A. Opala, S. Ghosh, L. Dominici, V. Ardizzone, M. De Giorgi, G. Lerario, G. Gigli, T. C. H. Liew, M. Matuszewski, D. Sanvitto
Polaritonic Neuromorphic Computing Outperforms Linear Classifiers
Nano Lett. 20, 3506−3512 (2020) DOI: 10.1021/acs.nanolett.0c00435, ArXiv: 1911.02923
- P. Comaron, V. Shahnazaryan, W. Brzezicki, T. Hyart, M. Matuszewski
Non-Hermitian topological end-mode lasing in polariton systems
Phys. Rev. Research 2, 022051(R) (2020) DOI: 10.1103/PhysRevResearch.2.022051, ArXiv: 1912.06431
- H. Xu, S. Ghosh, M. Matuszewski, T. C. H. Liew
Universal Self-Correcting Computing with Disordered Exciton-Polariton Neural Networks
Phys. Rev. Applied 13, 064074 (2020) DOI: 10.1103/PhysRevApplied.13.064074
- P. Comaron, V. Shahnazaryan, M. Matuszewski
Coherent transfer of topological interface states
Optics Express 28, 38698-38709 (2020) DOI: 10.1364/OE.409715, ArXiv: 2005.06281
- D. A. Nissley, Q. V. Vu, F. Trovato, N. Ahmed, Y. Jiang, M. S. Li, E. P. O’Brien
Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling
Journal of the American Chemical Society 142, 6103 (2020) DOI: 10.1021/jacs.9b12264
- K. Ho, D. T. Truong, M. S. Li
How Good is Jarzynski’s Equality for Computer-Aided Drug Design?
The Journal of Physical Chemistry B 124, 5338 (2020) DOI: 10.1021/acs.jpcb.0c02009
- D. Q. H. Pham, P. Krupa, H. L. Nguyen, G. L. Penna, M. S. Li
Computational Model to Unravel the Function of Amyloid-βPeptides in Contact with a Phospholipid membrane
The Journal of Physical Chemistry B 124, 3300 (2020) DOI: 10.1021/acs.jpcb.0c00771
- H. L. Nguyen, T. Q. Nguyen, D, T. Truong, M. S. Li
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) DOI: 10.1021/acs.jpcb.0c07312
- H. L. Nguyen, L. D. Pham, T. Q. Nguyen, D. A. Nissley, E. P. O’Brien, M. S. Li
Does SARS-CoV-2 Bind to Human ACE2 More Strongly Than Does SARS-CoV?
The Journal of Physical Chemistry B 124, 7336 (2020) DOI: 10.1021/acs.jpcb.0c04511
- H. L. Nguyen, H. Q. Linh, P. Matteini, G. L. Penna, M. S. Li
Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study
The Journal of Physical Chemistry B 124, 10617 (2020) DOI: 10.1021/acs.jpcb.0c05508
- A. M. Gabovich, M. S. Li, H. Szymczak, A. I. Voitenko
Electric dipole image forces in three-layersystems: The classical electrostatic model
The Journal of Chemical Physics 152, 094705 (2020) DOI: 10.1063/1.5142280
- T. C. Nguyen, L. D. Pham, D. Q. H. Pham, M. S. Li
Heat-induced degradation of fibrils: Exponential vs logistic kinetics
The Journal of Chemical Physics 152, 115101 (2020) DOI: 10.1063/1.5144305
- M. Gancar, K. Ho, Sk. A. Mohid, T. Q. Nguyen, Z. Bednarikova. H. L. Nguyen, A. Bhunia, E. Nepovimova, M. S. Li, Z. Gazova
7 Methoxytacrine and 2 Aminobenzothiazole Heterodimers: Structure−Mechanism Relationship of Amyloid Inhibitors Based on Rational Design
ACS Chemical Neuroscience 11, 715 (2020) DOI: 10.1021/acschemneuro.9b00419
- T. Q. Nguyen, P. E. Theodorakis, 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) DOI: 10.1021/acs.jcim.9b00834
- S. Boopathi, D. Q. H. Pham, W. Gonzalez, P. E. Theodorakis, M. S. Li
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) DOI: 10.1002/prot.25901
- M. Banchelli, R. Cascella, C. D'Andrea, L. Cabaj, I. Osticioli, D. Ciofini, M. S. Li, K. Skupień, M. D. Angelis, S. Siano, C. Cecchi, R. Pini, G. L. Penna, F. Chiti, P. Matteini
Nanoscopic insights into the surface conformation of neurotoxic amyloid β oligomers
The Royal Society of Chemistry Advances 10, 21907 (2020) DOI: 10.1039/D0RA03799K
- H. L. Nguyen, L. D. Pham, T. Q. Nguyen, D. A. Nissley, E. P. O’Brien, M. S. Li
Does SARS-CoV 2 Bind to Human ACE2 More Strongly Than Does SARS-CoV?
The Journal of Physical Chemistry B 124, 7336 (2020) DOI: 10.1021/acs.jpcb.0c04511
- V. M. Hoang, M. S. Li, P. Derreumaux, J. Wang, T. T. Nguyen, S. Nangia, P. H. Nguyen
Molecular mechanism of ultrasound interaction with a blood brain barrier model
The Journal of Chemical Physics 153, 045104 (2020) DOI: 10.1063/5.0010667
- T. Ekino, A. M. Gabovich, M. S. Li, 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) DOI: 10.1063/10.0000873
- E. Vatansever, S. D. Vatansever, P. E. Theodorakis, N. G. Fytas
Ising universality in the two-dimensional Blume-Capel model with quenched random crystal field
Phys. Rev. E 102, 062138 (2020) DOI: 10.1103/PhysRevE.102.062138, ArXiv: 2012.02437
- B. Liu, S.W. Wang, L. Chai, G. El Achkar, A. Chen, P. E. Theodorakis
Experimental investigation of nanoparticles distribution mechanisms and deposition patterns during nanofluid droplet evaporation
Eur. Phys. J. Appl. Phys. 92, 11101 (2020) DOI: 10.1051/epjap/2020200168
- P. Yatsyshin, N.G. Fytas, P. E. Theodorakis
Mixing-demixing transition in polymer-grafted spherical nanoparticles
Soft Matter 16, 703 (2020) DOI: 10.1039/C9SM01639B, ArXiv: 1908.01578
- 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) DOI: 10.1103/PhysRevLett.125.095301, ArXiv: 2004.00918
- R. P. A. Emmanuele, M. Sich, O. Kyriienko, V. Shahnazaryan, F. Withers, A. Catanzaro, P. M. Walker, F. A. Benimetskiy, M. S. Skolnick, A. I. Tartakovskii, I. A. Shelykh, D. N. Krizhanovskii
Highly nonlinear trion-polaritons in a monolayer semiconductor
Nature Communications 11, 3589 (2020) DOI: 10.1038/s41467-020-17340-z, ArXiv: 1910.14636
- 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) DOI: 10.1103/PhysRevB.102.115310, ArXiv: 2004.12896
- 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) DOI: 10.1002/sia.6705
- 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) DOI: 10.1088/1361-6455/ab81e9, ArXiv: 1911.12802
- H. Popova, F. Krzyżewski, M. A. Załuska-Kotur, V. Tonchev
Quantifying the Effect of Step−Step Exclusion on Dynamically Unstable Vicinal Surfaces: Step Bunching without Macrostep Formation
Crystal Growth & Design 20, 7246 (2020) DOI: 10.1021/acs.cgd.0c00927, ArXiv: 2001.08463
- A. Niezgoda, E. Witkowska, S. S. Mirkhalaf
Twist-and-store entanglement in bimodal and spin-1 Bose-Einstein condensates
Phys. Rev. A 102, 053315 (2020) DOI: 10.1103/PhysRevA.102.053315, ArXiv: 2009.07372
- S. S. Mirkhalaf, E. Witkowska, L. Lepori
Supersensitive quantum sensor based on criticality in an antiferromagnetic spinor condensate
Phys. Rev. A 101, 043609 (2020) DOI: 10.1103/PhysRevA.101.043609, ArXiv: 1912.02418
- M. Płodzień, M. Kościelski, E. Witkowska, A. Sinatra
Producing and storing spin-squeezed states and Greenberger-Horne-Zeilinger states in a one-dimensional optical lattice
Phys. Rev. A 102, 013328 (2020) DOI: 10.1103/PhysRevA.102.013328, ArXiv: 2005.02676
- R. Buczko, P. Kacman
Comment on Tuning topological surface states by cleavage angle in topological crystalline insulators
Phys. Rev. B 101, 157103 (2020) DOI: 10.1103/PhysRevB.101.157103
- T. Struck, A. Hollmann, F. Schauer, O. Fedorets, A. Schmidbauer, K. Sawano, H. Riemann, N. V. Abrosimov, Ł. Cywiński, D. Bougeard, L. R. Schreiber
Low-frequency spin qubit energy splitting noise in highly purified 28Si/SiGe
npj Quantum Information 6, 40 (2020) DOI: 10.1038/s41534-020-0276-2, ArXiv: 1909.11397
- J. A. Krzywda, Ł. Cywiński
Adiabatic electron charge transfer between two quantum dots in presence of 1/f noise
Phys. Rev. B 101, 035303 (2020) DOI: 10.1103/PhysRevB.101.035303, ArXiv: 1909.11780
- D. Kwiatkowski, P. Szańkowski, Ł. Cywiński
Influence of nuclear spin polarization on the spin-echo signal of an NV-center qubit
Phys. Rev. B 101, 155412 (2020) DOI: 10.1103/PhysRevB.101.155412, ArXiv: 1909.06438
- P. Szańkowski, Ł. Cywiński
Noise representations of open system dynamics
Sci. Rep. 10, 22189 (2020) DOI: 10.1038/s41598-020-78079-7, ArXiv: 2003.09688
- F. Sakuldee, Ł. Cywiński
Spectroscopy of classical environmental noise with a qubit subjected to projective measurements
Phys. Rev. A 101, 012314 (2020) DOI: 10.1103/PhysRevA.101.012314, ArXiv: 1907.01784
- F. Sakuldee, Ł. Cywiński
Relationship between subjecting the qubit to dynamical decoupling and to a sequence of projective measurements
Phys. Rev. A 101, 042329 (2020) DOI: 10.1103/PhysRevA.101.042329, ArXiv: 1907.05165
- M. Strzałka, D. Kwiatkowski, Ł. Cywiński, K. Roszak
Qubit-environment negativity versus fidelity of conditional environmental states for a nitrogen-vacancy-center spin qubit interacting with a nuclear environment
Phys. Rev. A 102, 042602 (2020) DOI: 10.1103/PhysRevA.101042602, ArXiv: 1911.08867
- N. V. Hung, P. Szańkowski, V. V. Konotop, M. Trippenbach
Four-wave mixing in spin–orbit coupled Bose–Einstein condensates
New J. Phys. 22, 053019 (2020) DOI: 10.1088/1367-2630/ab7fcb, ArXiv: 1901.06173
- I. Białynicki-Birula, Z. Białynicka-Birula
Comment on “Nondispersive analytical solutions to the Dirac equation”
Phys. Rev. Research 2, 038001 (2020) DOI: 10.1103/PhysRevResearch.2.038001, ArXiv: 2006.0761
- I. Białynicki-Birula, Z. Białynicka-Birula
Berry phase for spins of relativistic electrons
Acta Phys. Polon. A 138, 335 (2020) DOI: 10.12693/APhysPolA.138.335, ArXiv: 2009.07505
- I. Białynicki-Birula, Z. Białynicka-Birula
Three measures of fidelity for photon states
Phys. Rev. A 102, 042201 (2020) DOI: 10.1103/PhysRevA.102.042201, ArXiv: 2009.13842
- L. Li, J. Hu, B. Różycki, F. Song
Intercellular receptor-ligand binding and thermal fluctuations facilitate receptor aggregation in adhering membranes
Nano Lett. 20, 722 (2020) DOI: 10.1021/acs.nanolett.9b04596
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Pseudo-improper-dihedral model for intrinsically disordered proteins
J. Chem. Theory Comput. 16, 4726 (2020) DOI: 10.1021/acs.jctc.0c00338
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Quantum versus classical angular momentum
Eur. J. Phys. 41, 025402 (2020) DOI: 10.1088/1361-6404/ab4b2d, ArXiv: 1907.09930
- T. Karpiuk, M. Gajda, M. Brewczyk
Bistability of Bose-Fermi mixtures
New J Phys. 22, 103025 (2020) DOI: 10.1088/1367-2630/abbcef, ArXiv: 2004.07008
- M. Gajda, J. Mostowski, M. Pylak, T. Sowiński, M. Załuska-Kotur
Pauli crystals -- interplay of symmetries
Symmetry 12, 1886 (2020) DOI: 10.3390/sym12111886, ArXiv: 2009.04840
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Correlations in few two-component quantum walkers on a tilted lattice
Phys. Rev. A 102, 043326 (2020) DOI: 10.1103/PhysRevA.102.043326, ArXiv: 2006.13744
- P. Kościk, T. Sowiński
Variational ansatz for p-wave fermions confined in a one-dimensional harmonic trap
New J. Phys. 22, 093053 (2020) DOI: 10.1088/1367-2630/abb386, ArXiv: 2004.06610
- S. Sarkar, Ch. Mukhopadhyay, A. Bayat
Characterization of an operational quantum resource in a critical many-body system
New J. Phys. 22, 083077 (2020) DOI: 10.1088/1367-2630/aba919, ArXiv: 1908.08058
- F. Giacosa, P. Kościk, T. Sowiński
Capturing non-exponential dynamics in the presence of two decay channels
Phys. Rev. A 102, 022204 (2020) DOI: 10.1103/PhysRevA.102.022204, ArXiv: 1912.06394
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Interspecies entanglement with impurity atoms in a lattice gas
New J. Phys. 22, 083017 (2020) DOI: 10.1088/1367-2630/ab9fc1, ArXiv: 1805.01592
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Quantum walk versus classical wave: Distinguishing ground states of quantum magnets by spacetime dynamics
Phys. Rev. B 102, 024440 (2020) DOI: 10.1103/PhysRevB.102.024440, ArXiv: 2002.00812
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Simulating artificial one-dimensional physics with ultra-cold fermionic atoms: three exemplary themes
Adv. Quantum Technol. 3, 2000010 (2020) DOI: 10.1002/qute.202000010, ArXiv: 2001.04223
- D. Nandy, T. Sowiński
Dynamical properties of a few mass-imbalanced ultra-cold fermions confined in a double-well potential
New J. Phys. 22, 053043 (2020) DOI: 10.1088/1367-2630/ab878c, ArXiv: 1911.11539
- D. K. Nandy, M. Haque, A. E. B. Nielsen
Few-particle dynamics of fractional quantum Hall lattice models
Phys. Rev. B 101, 205305 (2020) DOI: 10.1103/PhysRevB.101.205305, ArXiv: 1912.09894
- D. Pęcak, T. Sowiński
Signatures of unconventional pairing in spin-imbalanced one-dimensional few-fermion systems
Phys. Rev. Research 2, 012077(R) (2020) DOI: 10.1103/PhysRevResearch.2.012077, ArXiv: 1911.04187
- P. Łydżba, T. Sowiński
Unconventional pairing in one-dimensional systems of a few mass-imbalanced ultra-cold fermions
Phys. Rev. A 101, 033603 (2020) DOI: 10.1103/PhysRevA.101.033603, ArXiv: 1911.04188
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Geometry-induced entanglement in a mass-imbalanced few-fermion system
Phys. Rev. A 101, 023604 (2020) DOI: 10.1103/PhysRevA.101.023604, ArXiv: 1909.08949
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