accessibility logoLow Vision accessibility
IFPAN

Division of Theoretical Physics

Institute of Physics, Polish Academy of Sciences

Home • People • Research • Publications • Grants • Seminars • Events • Join us

Scientific publications

2022

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. P. Szańkowski
    Measuring trajectories of environmental noise
    Phys. Rev. A 104, 022202 (2021)
    DOI: 10.1103/PhysRevA.104.022202, ArXiv: 2106.08434
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. M. Denys
    Model of cunning agents
    Physica A 574, 125987 (2021)
    DOI: 10.1016/j.physa.2021.125987, ArXiv: 2012.08517
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. Ł. Mioduszewski, B. Różycki, M. Cieplak
    Pseudo-improper-dihedral model for intrinsically disordered proteins
    J. Chem. Theory Comput. 16, 4726 (2020)
    DOI: 10.1021/acs.jctc.0c00338
  48. J. Mostowski, J. Pietraszewicz
    Quantum versus classical angular momentum
    Eur. J. Phys. 41, 025402 (2020)
    DOI: 10.1088/1361-6404/ab4b2d, ArXiv: 1907.09930
  49. 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
  50. 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
  51. S. Sarkar, T. Sowiński
    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
  52. 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
  53. 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
  54. 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
  55. S. Sarkar, S. McEndoo, D. Schneble, A. J. Daley
    Interspecies entanglement with impurity atoms in a lattice gas
    New J. Phys. 22, 083017 (2020)
    DOI: 10.1088/1367-2630/ab9fc1, ArXiv: 1805.01592
  56. P. Wrzosek, K. Wohlfeld, D. Hofman, T. Sowiński, M. A. Sentef
    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
  57. J. Dobrzyniecki, T. Sowiński
    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
  58. 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
  59. 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
  60. 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
  61. 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
  62. D. Włodzyński, D. Pęcak, T. Sowiński
    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
Valid XHTML 1.0 Transitional
design & code: T. Sowiński