Article
Biochemistry & Molecular Biology
Harutyun Sahakyan, Karen Nazaryan, Arcady Mushegian, Irina Sorokina
Summary: Molecular dynamics simulations were performed to study protein folding. By applying rotational force to the C-terminal amino acid while restricting the movement of the N-terminal amino acid, the folding of four protein domains was accelerated at least by an order of magnitude. These results suggest that external forces and constraints can bias the motions of the polypeptide and facilitate the attainment of stable fold.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
M. Benelmekki, V Singh, K. W. Baughman, M. Bohra, J-H Kim
Summary: A templateless physical method was employed to generate FeAg-based anisotropic nanostructures, leading to the successful magnetic-assisted assembly of Fe nanoclusters and various Fe nanostructures under tuned experimental conditions. The assembly process is driven by the interplay between magnetic interaction energy and overall surface energy, resulting in the formation of stable and permanent branched nanostructures.
MATERIALS TODAY CHEMISTRY
(2021)
Article
Materials Science, Multidisciplinary
Laura Friedeheim, Nicholas P. Bailey, Jeppe C. Dyre
Summary: This paper presents computer simulations of CuxZr100-x alloys in the liquid and glass phases, finding good invariance of both structure and dynamics in reduced units. Results show that the liquid and glass parts of the thermodynamic phase diagram of this metallic glass former at a fixed composition are effectively one-dimensional, with many physical properties remaining invariant along isochores.
Article
Chemistry, Physical
Stephan J. Schmutzler, Adrian Ruckhofer, Wolfgang E. Ernst, Anton Tamtoegl
Summary: The surface of Bi(114) is a notable example where reduced dimensionality leads to structural rearrangement and new states. Through helium atom scattering (HAS) measurements, we present a study of the surface structure and electronic corrugation of this quasi one-dimensional topological metal. Unlike low-index metal surfaces, scattering from the stepped (114) truncation of Bi results in a significant amount of the incident beam being scattered into higher order diffraction channels, making the analysis challenging.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Mathieu Roule, Jean-Baptiste Fouvry, Christophe Pichon, Pierre-Henri Chavanis
Summary: In this study, we investigate the long-term relaxation of one-dimensional self-gravitating systems using both kinetic theory and N-body simulations. Our findings show that all combinations of thermal and Plummer equilibria, with or without collective effects, are consistent with the predictions of Balescu-Lenard and Landau for diffusion coefficients. Interestingly, collective effects reduce diffusion by a factor of about 10. The predicted flux for Plummer equilibrium matches the measured one, providing a remarkable validation of kinetic theory. We also observe a case of quasikinetic blocking for the same equilibrium.
Article
Materials Science, Multidisciplinary
Onuttom Narayan, Harsh Mathur, Richard Montgomery
Summary: The study reveals that a one-dimensional disordered conductor with correlated disorder has an extended state and a Landauer resistance that is non-zero in the limit of infinite system size, contrary to the predictions of Anderson localization scaling theory. The delocalization transition is not related to any underlying symmetry of the model, and the form of correlated disorder is different from other models with delocalization transitions discussed in the literature. For a wire of finite length, this effect manifests as a sharp transmission resonance that narrows as the length of the wire increases.
Article
Physics, Multidisciplinary
Mu Qiao, Ye Wang, Zhengyang Cai, Botao Du, Pengfei Wang, Chunyang Luan, Wentao Chen, Heung-Ryoul Noh, Kihwan Kim
Summary: The study investigates double-electromagnetically-induced transparency (double-EIT) cooling of ion crystals in a Paul trap, demonstrating efficient ground-state cooling. The experimental results match theoretical predictions in terms of cooling rate and limit. This method could be extended to other ions and may advance the field of quantum information sciences by enabling near ground-state cooling of stationary ion crystals with large numbers of ions.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Jacob D. Marold, Kevin Sforza, Kathryn Geiger-Schuller, Tural Aksel, Sean Klein, Mark Petersen, Ekaterina Poliakova-Georgantas, Doug Barrick
Summary: A collection of programs is presented for analyzing the thermodynamics of folding of linear repeat proteins using a 1D Ising model. These programs determine intrinsic folding and interfacial coupling free energies, and are designed to analyze Ising parameters for homopolymeric and heteropolymeric constructs. The programs also provide a bootstrap analysis for estimating parameter uncertainty and correlations among fitted parameters. Rigorous statistical analysis is essential for interpreting the fits obtained from the complex Ising analysis of repeat proteins.
Article
Multidisciplinary Sciences
Adrian Del Maestro, Nathan S. Nichols, Timothy R. Prisk, Garfield Warren, Paul E. Sokol
Summary: This article demonstrates the quantum one-dimensional behavior of helium confined in nanopores using neutron scattering. The confined helium-4 exhibits qualitatively different excitations compared to bulk superfluid helium, and can be characterized by a mobile impurity.
NATURE COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Peilong Liao, Jianbin Huang, Yun Yan, Ben Zhong Tang
Summary: Clusterization-triggered emission (CTE) is a photophysical phenomenon that allows for highly efficient light emission from non-conjugated molecules. Applications of CTE include optical anti-counterfeiting, white LED materials, bioimaging, and molecular sensing. In the future, CTE may revolutionize the design of advanced functional luminescent materials.
MATERIALS CHEMISTRY FRONTIERS
(2021)
Article
Chemistry, Physical
Shanshan Wu, Huiyu Li, Ao Ma
Summary: Understanding the mechanism of functional protein dynamics is crucial for understanding protein functions. A new method using the generalized work functional has been proposed to identify the one-dimensional reaction coordinate (1D-RC) in complex molecules, which can accurately determine the reaction probability.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Applied
Zehua Huang, Luyan Huang, Weikun Chen, Jian Jing, Xuefeng Liang, Lisheng Zhang, Yuanzheng Tang, Zhiming Liu, Yan He, Huifang Li
Summary: This study investigates the diffusion behaviors of different gas molecules in the channels of AlPO4-5 zeolite-like material using MD simulations and DFT calculations. The results show that light molecules have more freedom for diffusion at low loading, while heavier molecules are controlled by gas-gas and gas-porous media interactions at high loading.
MICROPOROUS AND MESOPOROUS MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Zhenguang Zhao, Reem Mousa, Norman Metanis
Summary: SELENOF is an endoplasmic reticulum selenoprotein that may be responsible for reducing non-native disulfide bonds in misfolded glycoproteins.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Physics, Applied
P. Dumas, P. -L. Julliard, J. Borrel, S. Duguay, F. Hilario, F. Deprat, V. Lu, W. Zhao, W. Zou, E. Arevalo, D. Blavette
Summary: Carbon was co-implanted with phosphorus in silicon at a low temperature, resulting in increased phosphorus activation due to the suppression of extended defects. The formation of carbon clusters composed of immobile dimers carbon/self-interstitials, in agreement with the stoichiometry of the SiC phase, was observed. A temperature window (>750 degrees C) where self-interstitials are trapped by carbon was found based on the model presented.
JOURNAL OF APPLIED PHYSICS
(2021)
Article
Physics, Applied
Alexander S. Balankin, M. A. Martinez-Cruz, E. Reyes de Luna
Summary: The effects of geometric confinement on random walks and diffusion processes in systems of reduced dimensionality are studied in this work. Monte Carlo simulations reveal that the crossover behavior from two- to one-dimensional diffusion in the Fickian regime is controlled by the ratio of strip width to the standard deviation of the walker step length distribution, with the characteristic time scaling quadratically with this ratio.
MODERN PHYSICS LETTERS B
(2022)
Article
Multidisciplinary Sciences
Yuzuru Itoh, Juni Andrell, Austin Choi, Uwe Richter, Priyanka Maiti, Robert B. Best, Antoni Barrientos, Brendan J. Battersby, Alexey Amunts
Summary: The study reveals the mechanism of interaction between human mitoribosomes and the insertase OXA1L, elucidating how membrane delivery is achieved during protein synthesis.
Article
Biochemistry & Molecular Biology
Joan-Emma Shea, Robert B. Best, Jeetain Mittal
Summary: Intrinsically disordered proteins (IDPs) are a special class of proteins that do not fold into specific 3D shapes, making experimental studies challenging and requiring theoretical and computational methods. Recent progress has been made in developing new computational and theoretical approaches to study the structure and dynamics of IDPs, particularly their phase separation into protein-rich condensates.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Chemistry, Physical
Grace H. Taumoefolau, Robert B. Best
Summary: In a two-state molecular system, transition paths involve the trajectories during which the system transitions between stable states. Single-molecule experiments can estimate transition-path durations, although there may be a tendency to underestimate. Greater flexibility in the transition-path model can lead to more accurate extraction of transition-path times.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Thomas Dannenhoffer-Lafage, Robert B. Best
Summary: Recent evidence suggests that liquid-liquid phase separation (LLPS) plays a key role in the formation of membraneless organelles, while the development of a new, data-driven hydrophobicity scale can better predict protein phase separation behavior under physiological conditions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemical Research Methods
Paulo C. T. Souza, Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grunewald, Ilias Patmanidis, Haleh Abdizadeh, Bart M. H. Bruininks, Tsjerk A. Wassenaar, Peter C. Kroon, Josef Melcr, Vincent Nieto, Valentina Corradi, Hanif M. Khan, Jan Domanski, Matti Javanainen, Hector Martinez-Seara, Nathalie Reuter, Robert B. Best, Ilpo Vattulainen, Luca Monticelli, Xavier Periole, D. Peter Tieleman, Alex H. de Vries, Siewert J. Marrink
Summary: The refined Martini 3 model offers improved interaction balance and expanded ability to include specific interactions, allowing for more accurate predictions of molecular packing and interactions. It has been successfully applied in a wide range of applications, demonstrating its versatility and effectiveness in biomolecular simulations.
Article
Chemistry, Multidisciplinary
Mark F. Nueesch, Milos T. Ivanovic, Jean-Benoit Claude, Daniel Nettels, Robert B. Best, Jerome Wenger, Benjamin Schuler
Summary: The use of nanophotonic fluorescence enhancement in zero-mode waveguides dramatically improves time resolution and reduces data acquisition times, enabling measurement of previously inaccessible low-nanosecond dynamics in biomolecules. This approach allows for better detection of biomolecular dynamics and achieves highly consistent results with all-atom molecular dynamics simulations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Petur O. Heidarsson, Davide Mercadante, Andrea Sottini, Daniel Nettels, Madeleine B. Borgia, Alessandro Borgia, Sinan Kilic, Beat Fierz, Robert B. Best, Benjamin Schuler
Summary: This article reports a new mechanism of molecular competition that explains the role of highly charged intrinsically disordered proteins in chromatin structure and transcriptional activity regulation. This mechanism utilizes the pronounced dynamical disorder of these proteins and their complexes, allowing a highly negatively charged histone chaperone to efficiently invade and displace a highly positively charged histone bound to a nucleosome, thereby accelerating its dissociation.
Article
Chemistry, Physical
Kathryn M. Lebold, Robert B. Best
Summary: The high concentration of nucleic acids and positively charged proteins in the cell nucleus provides many possibilities for complex coacervation. The variation of the positions of charged residues in proteins can tune the phase separation and affect the local ordering and the ordering of DNA.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Sai Chaitanya Chiliveri, John M. Louis, Robert B. Best, Ad Bax
Summary: This study measured the dynamic equilibrium of the HIV-1 virus envelope glycoprotein gp41 in the presence of lipid mimics and determined the reaction kinetics and energy associated with its lipid-bound intermediate and post-fusion six-helical bundle states. The findings provide important insights into the molecular basis of viral membrane fusion.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Pengfei Tian, Adrien Lemaire, Fabien Senechal, Olivier Habrylo, Viviane Antonietti, Pascal Sonnet, Valerie Lefebvre, Frederikke Isa Marin, Robert B. Best, Jerome Pelloux, Davide Mercadante
Summary: Efficiently designing functional proteins with higher thermal stability is still challenging, especially for highly diverse sequence variants. However, optimizing sequence design based on evolutionary fitness can help improve protein stability. In this study, we used a generative evolution fitness model to design artificial sequences for a proteinaceous inhibitor of pectin methylesterase enzymes. The majority of the designs were functional, and some even showed improved thermal stability. This method has the potential to expand the sequence space of functional proteins with valuable traits for industrial applications and scientific research.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Meeting Abstract
Biophysics
Kathryn M. Lebold, Robert B. Best
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Robert B. Best
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Thomas P. Dannenhoffer-Lafage, Robert B. Best
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Layne B. Frechette, Robert B. Best
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Grace H. Taumoefolau, Robert B. Best
BIOPHYSICAL JOURNAL
(2022)