Journal of Chemical Physics最新文献_第9页

Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0250082

Hindol Chatterjee, Pallab Dutta, Martin Zacharias, Neelanjana Sengupta

{"title":"Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence.","authors":"Hindol Chatterjee, Pallab Dutta, Martin Zacharias, Neelanjana Sengupta","doi":"10.1063/5.0250082","DOIUrl":"https://doi.org/10.1063/5.0250082","url":null,"abstract":"Membrane protein folding in the viscous microenvironment of a lipid bilayer is an inherently slow process that challenges experiments and computational efforts alike. The folding kinetics is moreover associated with topological modulations of the biological milieu. Studying such structural changes in membrane-embedded proteins and understanding the associated topological signatures in membrane leaflets, therefore, remain relatively unexplored. Herein, we first aim to estimate the free energy barrier and the minimum free energy path (MFEP) connecting the membrane-embedded fully and partially inserted states of the bacteriorhodopsin fragment. To achieve this, we have considered independent sets of simulations from membrane-mimicking and membrane-embedded environments, respectively. An autoencoder model is used to elicit state-distinguishable collective variables for the system utilizing membrane-mimicking simulations. Our in-house Expectation Maximized Molecular Dynamics algorithm is initially used to deduce the barrier height between the two membrane-embedded states. Next, we develop the Geometry Optimized Local Direction search as a post-processing algorithm to identify the MFEP and the corresponding peptide conformations from the autoencoder-projected trajectories. Finally, we apply a graph attention neural network (GAT) model to learn the membrane surface topology as a function of the associated peptide structure, supervised by the membrane-embedded simulations. The resultant GAT model is then utilized to predict the membrane leaflet topology for the peptide structures along MFEP, obtained from membrane-mimicking simulations. The combined framework is expected to be useful in capturing key phenomena accompanying folding transitions in membranes. We discuss opportunities and avenues for further development.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hamiltonian replica-exchange method α-REMD for ring spearing elimination in polymers.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0241538

Artem Yu Kunitsyn, Nadezhda A Nekrasova, Nikolai V Krivoshchapov, Eugeny V Alexandrov, Alexander A Pavlov, Michael G Medvedev

{"title":"Hamiltonian replica-exchange method α-REMD for ring spearing elimination in polymers.","authors":"Artem Yu Kunitsyn, Nadezhda A Nekrasova, Nikolai V Krivoshchapov, Eugeny V Alexandrov, Alexander A Pavlov, Michael G Medvedev","doi":"10.1063/5.0241538","DOIUrl":"https://doi.org/10.1063/5.0241538","url":null,"abstract":"Accurate prediction of polymer properties using molecular dynamics (MD) simulations requires a properly relaxed starting structure. Polymer models built from scratch by specialized algorithms (self-avoiding random walk, Monte Carlo, etc.) are far from relaxed and, moreover, often possess a large number of structural defects: close contacts between atoms, wrong bond distances, voids, unfavorable molecular conformations or packing, etc. This is especially problematic for ring-containing polymers whose initial structures also include ring spearing (bonds passing through cycles, including benzene rings). All these defects must be eliminated before running an MD simulation to correctly predict polymer properties. Short MD simulations can be enough to remove close contacts; however, ring spearing elimination and general structure relaxation cannot be achieved this way. In this work, we propose α-Replica Exchange MD (α-REMD)-a Hamiltonian replica-exchange MD protocol that reliably eliminates ring spearing defects and performs a general relaxation of the system. Its efficiency is demonstrated on five polyethersulfones whose initial geometries contained numerous ring intersections that were completely removed by α-REMD.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coherent control of the efficient ladder-type population transfer by four-color harmonic laser pulses. 四色谐波激光脉冲对高效阶梯型种群转移的相干控制。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0253782

Bin-Bin Wang, Yuan Li, Su-Hua Jing, Xiao-Yun Zhou, Yong-Chang Han

{"title":"Coherent control of the efficient ladder-type population transfer by four-color harmonic laser pulses.","authors":"Bin-Bin Wang, Yuan Li, Su-Hua Jing, Xiao-Yun Zhou, Yong-Chang Han","doi":"10.1063/5.0253782","DOIUrl":"https://doi.org/10.1063/5.0253782","url":null,"abstract":"The ladder-type population transfer of the HF molecule steered by four-color harmonic laser pulses (HLPs) is investigated using the time-dependent quantum wave packet method. It is found that although there exist large background excitations and many (resonant) transition pathways during the driving, nearly 100% of the population could be transferred to the target state. In particular, such a process could be coherently controlled by changing the phases of the four HLPs, especially the phases of the fundamental and second HLPs, which can be accounted for in large part by the combined effects of the corresponding transition pathways and the maximal amplitude of the total electric field. However, for manipulating the phases of the third and fourth HLPs, both the changes in the maximal electric field amplitude and the asymmetry size fail to guide the variation of the target-state population because of the correlated effects of all these transition pathways, particularly the ones that do not contain the third and fourth HLP excitations. Importantly, our results also denote that the variation of the maximal electric field amplitude may give a well qualitative prediction about the phase-controlled population when the manipulated phase is directly related to all the transition pathways, which is the general case in the widely used two-color scheme. In addition, the maximal amplitude of the total electric field tends to play a more important role than its asymmetry size in the phase-controlled population transfer process.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A relativistic third-order algebraic diagrammatic construction theory for electron detachment, attachment, and excitation problems.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0246920

Sudipta Chakraborty, Tamoghna Mukhopadhyay, Malaya K Nayak, Achintya Kumar Dutta

引用次数: 0

Langevin integration for isothermal-isobaric condition with a large time step.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0251642

Jaewoon Jung, Yuji Sugita

引用次数: 0

Stereodynamics of cold HD and D2 collisions with He.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0250522

Bikramaditya Mandal, Konrad Patkowski, Pablo G Jambrina, F Javier Aoiz, Naduvalath Balakrishnan

{"title":"Stereodynamics of cold HD and D2 collisions with He.","authors":"Bikramaditya Mandal, Konrad Patkowski, Pablo G Jambrina, F Javier Aoiz, Naduvalath Balakrishnan","doi":"10.1063/5.0250522","DOIUrl":"https://doi.org/10.1063/5.0250522","url":null,"abstract":"We present a comprehensive quantum mechanical study of stereodynamic control of HD + He and D2 + He collisions that have been probed experimentally by Perreault et al. [J. Phys. Chem. Lett. 13, 10912 (2022)] using Stark-induced adiabatic Raman passage (SARP) techniques. Our calculations utilize a highly accurate full-dimensional H2 + He interaction potential with diagonal Born-Oppenheimer correction appropriate for HD and D2 isotopomers. The results show that rotational quenching of HD from j = 2 → j' = 0 in v = 2, j = 2 → j' = 1 in v = 2 and v = 4, and j = 4 → j' = 3 in v = 4 is dominated by an l = 1 shape resonance located between 0.1 and 1.0 cm-1. For collision energies less than 0.1 cm-1, isotropic scattering prevails. An l = 1 resonance centered around 0.02 cm-1 is also found to dominate the j = 2 → j' = 0 and j = 4 → j' = 2 transitions in v = 4 for He-D2 collisions consistent with our prior studies of Δj = -2 transition in He + D2(v = 2, j = 2) collisions. Our analysis does not support the hypothesis of Perreault et al. [J. Phys. Chem. Lett. 13, 10912 (2022)] that a strong l = 2 resonance controls the angular distribution for Δj = -2 transition for both systems. Despite improvements in the development of the potential energy surface, a good agreement with SARP experiments for v = 2 is achieved only when contributions from collision energies less than 1.0 cm-1 were excluded in the computation of velocity averaged differential rate coefficients for both systems. This could be due to some uncertainties in the velocity spread in the experiment that employs co-propagation of the collision partners and possibly, the neglect of transverse velocities in the simulation of the experiment.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 10","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantum electrodynamic corrections for molecules: Vacuum polarization and electron self-energy in a two-component relativistic framework.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0252409

Kjell Janke, Andrés Emilio Wedenig, Peter Schwerdtfeger, Konstantin Gaul, Robert Berger

引用次数: 0

Controlling bulk electrostatics in electrolytes by surface polarization.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-14 DOI: 10.1063/5.0253254

Ralf Blossey, Rudolf Podgornik

引用次数: 0

Attaining high accuracy for charge-transfer excitations in non-covalent complexes at second-order perturbation cost: The importance of state-specific self-consistency.