Journal of Chemical Physics最新文献_第5页

Intrinsic hydrophobicity of IDP-based biomolecular condensates drives their partial drying on membrane surfaces.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0253522

J Holland, T J Nott, D G A L Aarts

{"title":"Intrinsic hydrophobicity of IDP-based biomolecular condensates drives their partial drying on membrane surfaces.","authors":"J Holland, T J Nott, D G A L Aarts","doi":"10.1063/5.0253522","DOIUrl":"10.1063/5.0253522","url":null,"abstract":"The localization of biomolecular condensates to intracellular membrane surfaces has emerged as an important feature of sub-cellular organization. In this work, we study the wetting behavior of biomolecular condensates on various substrates. We use confocal microscopy to measure the contact angles of model condensates formed by intrinsically disordered protein Ddx4N. We show the importance of taking optical aberrations into account, as these impact apparent contact angle measurements. Ddx4N condensates are seen to partially dry (contact angles above 90°) a model membrane, with little dependence on the magnitude of charge on, or tyrosine content of, Ddx4N. Further contact angle measurements on surfaces of varying hydrophilicity reveal a preference of Ddx4N condensates for hydrophobic surfaces, suggesting an intrinsic repulsion between protein condensates and hydrophilic membrane surfaces. This observation is in line with previous studies relating protein adsorption to surface hydrophilicity. Our work advances the understanding of the molecular details governing the localization of biomolecular condensates.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mid-infrared strong nonreciprocal thermal radiation with extremely small applied magnetic field.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0262471

Jun Wu, Ye Ming Qing

引用次数: 0

Modeling entanglement dynamics of molecules interacting with entangled photons through Lindblad master equation approach.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0254272

Sajal Kumar Giri, George C Schatz

引用次数: 0

Perturbation of water-ethanol solvent structural relaxation by a bis-urea supramolecular gel and paracetamol.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0252501

Riccardo Morbidini, Robert M Edkins, Kirill Nemkovskiy, Gøran Nilsen, Tilo Seydel, Katharina Edkins

引用次数: 0

Revisiting the question of what instantaneous normal modes tell us about liquid dynamics.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0239061

Sha Jin, Xue Fan, Matteo Baggioli

{"title":"Revisiting the question of what instantaneous normal modes tell us about liquid dynamics.","authors":"Sha Jin, Xue Fan, Matteo Baggioli","doi":"10.1063/5.0239061","DOIUrl":"https://doi.org/10.1063/5.0239061","url":null,"abstract":"The lack of a well-defined equilibrium reference configuration has long hindered a comprehensive atomic-level understanding of liquid dynamics and properties. The Instantaneous Normal Mode (INM) approach, which involves diagonalizing the Hessian matrix of potential energy in instantaneous liquid configurations, has emerged as a promising framework in this direction. However, several conceptual challenges remain, particularly related to the approach's inability to capture anharmonic effects. In this study, we present a set of \"experimental facts\" through a comprehensive INM analysis of simulated systems, including Ar, Xe, N2, CS2, Ga, and Pb, across a wide temperature range from the solid to gas phase. First, we examine the INM density of states (DOS) and compare it to the DOS obtained from the velocity auto-correlation function. We then analyze the temperature dependence of the fraction of unstable modes and the low-frequency slope of the INM DOS in search of potential universal behaviors. Furthermore, we explore the relationship between INMs and other properties of liquids, including the liquid-like to gas-like dynamical crossover and the momentum gap of collective shear waves. In addition, we investigate the INM spectrum at low temperatures as the system approaches the solid phase, revealing a significant fraction of unstable modes even in crystalline solids. Finally, we confirm the existence of a recently discussed cusp-like singularity in the INM eigenvalue spectrum and uncover its complex temperature-dependent behavior, challenging current theoretical models.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657399","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

Non-perturbative exciton transfer rate analysis of the Fenna-Matthews-Olson photosynthetic complex under reducing and oxidizing conditions.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0251613

Hallmann Ó Gestsson, Charlie Nation, Jacob S Higgins, Gregory S Engel, Alexandra Olaya-Castro

{"title":"Non-perturbative exciton transfer rate analysis of the Fenna-Matthews-Olson photosynthetic complex under reducing and oxidizing conditions.","authors":"Hallmann Ó Gestsson, Charlie Nation, Jacob S Higgins, Gregory S Engel, Alexandra Olaya-Castro","doi":"10.1063/5.0251613","DOIUrl":"https://doi.org/10.1063/5.0251613","url":null,"abstract":"Two-dimensional optical spectroscopy experiments have examined photoprotective mechanisms in the Fenna-Matthews-Olson (FMO) photosynthetic complex, showing that exciton transfer pathways change significantly depending on the environmental redox conditions. Higgins et al. [Proc. Natl. Acad. Sci. U. S. A. 118(11), e2018240118 (2021)] have theoretically linked these observations to changes in a quantum vibronic coupling, whereby onsite energies are altered under oxidizing conditions such that exciton energy gaps are detuned from a specific vibrational motion of the bacteriochlorophyll a. These arguments rely on an analysis of exciton transfer rates within Redfield theory, which is known to provide an inaccurate description of the influence of the vibrational environment on the exciton dynamics in the FMO complex. Here, we use a memory kernel formulation of the hierarchical equations of motion to obtain non-perturbative estimations of exciton transfer rates, which yield a modified physical picture. Our findings indicate that onsite energy shifts alone do not reproduce the reported rate changes in the oxidative environment. We systematically examine a model that includes combined changes in both site energies and the frequency of a local vibration in the oxidized complex while maintaining consistency with absorption spectra and achieving qualitative, but not quantitative, agreement with the measured changes in transfer rates. Our analysis points to potential limitations of the FMO electronic Hamiltonian, which was originally derived by fitting spectra to perturbative theories. Overall, our work suggests that further experimental and theoretical analyses may be needed to understand the variations of exciton dynamics under different redox conditions.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657405","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

The synergy between compartmentalization and motorization in chromatin architecture.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0239634

Ronaldo J Oliveira, Antonio B Oliveira Junior, Vinícius G Contessoto, José N Onuchic

{"title":"The synergy between compartmentalization and motorization in chromatin architecture.","authors":"Ronaldo J Oliveira, Antonio B Oliveira Junior, Vinícius G Contessoto, José N Onuchic","doi":"10.1063/5.0239634","DOIUrl":"https://doi.org/10.1063/5.0239634","url":null,"abstract":"High-resolution techniques capable of manipulating from single molecules to millions of cells are combined with three-dimensional modeling followed by simulation to comprehend the specific aspects of chromosomes. From the theoretical perspective, the energy landscape theory from protein folding inspired the development of the minimal chromatin model (MiChroM). In this work, two biologically relevant MiChroM energy terms were minimized under different conditions, revealing a competition between loci compartmentalization and motor-driven activity mechanisms in chromatin folding. Enhancing the motor activity energy baseline increased the lengthwise compaction and reduced the polymer entanglement. Concomitantly, decreasing compartmentalization-related interactions reduced the overall polymer collapse, although compartmentalization given by the microphase separation remained almost intact. For multiple chromosome simulations, increased motorization intensified the territory formation of the different chains and reduced compartmentalization strength lowered the probability of contact formation of different loci between multiple chains, approximating to the experimental inter-contacts of the human chromosomes. These findings have direct implications for experimental data-driven chromosome modeling, specially those involving multiple chromosomes. The interplay between phase-separation and territory formation mechanisms should be properly implemented in order to recover the genome architecture and dynamics, features that might play critical roles in regulating nuclear functions.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657450","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

On the applicability of CCSD(T) for dispersion interactions in large conjugated systems.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0246763

S Lambie, D Kats, D Usvyat, A Alavi

{"title":"On the applicability of CCSD(T) for dispersion interactions in large conjugated systems.","authors":"S Lambie, D Kats, D Usvyat, A Alavi","doi":"10.1063/5.0246763","DOIUrl":"https://doi.org/10.1063/5.0246763","url":null,"abstract":"In light of the recent discrepancies reported between fixed node diffusion Monte Carlo and local natural orbital coupled cluster with single, double, and perturbative triples [CCSD(T)] methodologies for non-covalent interactions in large molecular systems [Al-Hamdani et al., Nat. Commun. 12, 3927 (2021)], the applicability of CCSD(T) is assessed using a model framework. The use of the semi-empirical π-space only Pariser-Parr-Pople (PPP) model for studying large molecules is critically examined and is shown to recover both bandgap closure as system size increases and long range dispersive behavior of r-6 with increasing separation between monomers. Since bandgap closure in systems with long-range Coulomb interactions is problematic for perturbative methods, such as CCSD(T), this model, therefore, serves as a testing ground for such methods, enabling them to be benchmarked with high-order CC methods, which are not possible with ab initio Hamiltonians. Using the PPP model, coupled cluster methodologies, CCSDTQ and CCSDT(Q), are then used to benchmark CCSDT and CCSD(T) methodologies for non-covalent interactions in large one- and two-dimensional molecular systems up to the dibenzocoronene dimer. We show that CCSD(T) demonstrates no signs of overestimating the interaction energy for these systems. Furthermore, by examining the Hartree-Fock HOMO-LUMO gap of these large molecules, the perturbative treatment of the triples contribution in CCSD(T) is not expected to cause problems for accurately capturing the interaction energy for system sizes up to at least circumcoronene.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657407","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

Unraveling internal friction in a coarse-grained protein model.

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0255498

Carlos Monago, J A de la Torre, R Delgado-Buscalioni, Pep Español

{"title":"Unraveling internal friction in a coarse-grained protein model.","authors":"Carlos Monago, J A de la Torre, R Delgado-Buscalioni, Pep Español","doi":"10.1063/5.0255498","DOIUrl":"https://doi.org/10.1063/5.0255498","url":null,"abstract":"Understanding the dynamic behavior of complex biomolecules requires simplified models that not only make computations feasible but also reveal fundamental mechanisms. Coarse-graining (CG) achieves this by grouping atoms into beads, whose stochastic dynamics can be derived using the Mori-Zwanzig formalism, capturing both reversible and irreversible interactions. In liquid, the dissipative bead-bead interactions have so far been restricted to hydrodynamic couplings. However, friction does not only arise from the solvent but, notably, from the internal degrees of freedom missing in the CG beads. This leads to an additional \"internal friction\" whose relevance is studied in this contribution. By comparing with all-atom molecular dynamics (MD), we neatly show that in order to accurately reproduce the dynamics of a globular protein in water using a CG model, not only a precise determination of elastic couplings and the Stokesian self-friction of each bead is required. Critically, the inclusion of internal friction between beads is also necessary for a faithful representation of protein dynamics. We propose to optimize the parameters of the CG model through a self-averaging method that integrates the CG dynamics with an evolution equation for the CG parameters. This approach ensures that selected quantities, such as the radial distribution function and the time correlation of bead velocities, match the corresponding MD values.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663599","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 bilinear model for the elastic response of hydrated lipid bilayers under normal pressure difference. 水合脂质双分子层在正常压差下的弹性响应双线性模型。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-03-21 DOI: 10.1063/5.0226774

A Farhangian, L Cowley, Y Dubief

{"title":"A bilinear model for the elastic response of hydrated lipid bilayers under normal pressure difference.","authors":"A Farhangian, L Cowley, Y Dubief","doi":"10.1063/5.0226774","DOIUrl":"https://doi.org/10.1063/5.0226774","url":null,"abstract":"The elasticity of phospholipid membranes as a function of hydration was investigated using coarse-grained molecular simulations. Multilamellar membranes consist of two or more lipid bilayers separated by a thin layer of water, a system commonly found in cell membranes that provides surface tension in the alveoli of the lungs and on cartilaginous surfaces of synovial joints. The objective was to quantify the response of such systems to compression in the direction perpendicular to the membranes as a function of the amount of water between the bilayers or hydration of the system. The present study investigated a variety of phospholipids with six levels of hydration found in multilamellar bilayers in biological systems. Our simulations support the existence of a universal behavior of the increase in surface area per lipid as a function of the normal pressure difference, the difference between the pressure applied in the direction normal to the membrane and the pressure applied in the directions parallel to the membrane. Normalizing the surface area per lipid and the pressure difference by their respective values at rupture yields a composite function of two linear regimes for all the hydration levels under investigation. Where possible, a physics-based interpretation of the normalization scales was provided. Although some parameters of the model are determined empirically, the model represents a promising step in continuum modeling of the response of multilamellar lipid membranes as a function of mechanical stress and hydration.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657313","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