Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field.

Sugars are ubiquitous in biology; they occur in all kingdoms of life. Despite their prevalence, they have often been somewhat neglected in studies of structure-dynamics-function relationships of macromolecules to which they are attached, with the exception of nucleic acids. This is largely due to the inherent difficulties of not only studying the conformational dynamics of sugars using experimental methods but indeed also resolving their static structures.

Amoeba Monte Carlo algorithms for random trees with controlled branching activity: Efficient trial move generation and universal dynamics.

The reptation Monte Carlo algorithm is a simple, physically motivated and efficient method for equilibrating semidilute solutions of linear polymers. Here, we propose two simple generalizations for the analog Amoeba algorithm for randomly branching chains, which allow us to efficiently deal with random trees with controlled branching activity. We analyze the rich relaxation dynamics of Amoeba algorithms and demonstrate the existence of an unexpected scaling regime for the tree relaxation.

OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field.

Coarse-grained molecular dynamics simulations enable the modeling of increasingly complex systems at millisecond timescales. The transferable coarse-grained force field Martini 3 has shown great promise in modeling a wide range of biochemical processes, yet folded proteins in Martini 3 are not stable without the application of external bias potentials, such as elastic networks or Go̅-like models. We herein develop an algorithm, called OLIVES, which identifies native contacts with hydrogen bond capabilities in coarse-grained proteins and use it to implement a novel Go̅-like model for Martini 3.

Depletion of membrane cholesterol modifies structure, dynamic and activation of Na1.7.

Cholesterol is a major component of plasma membranes and plays a significant role in actively regulating the functioning of several membrane proteins in humans. In this study, we focus on the role of cholesterol depletion on the voltage-gated sodium channel Na1.7, which is primarily expressed in the peripheral sensory neurons and linked to various chronic inherited pain syndromes.

Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics.

Coarse-grained (CG) molecular dynamics (MD) simulations have grown in applicability over the years. The recently released version of the Martini CG force field (Martini 3) has been successfully applied to simulate many processes, including protein-ligand binding. However, the current ligand parametrization scheme is manual and requires an a priori reference all-atom (AA) simulation for benchmarking.

Bending of a lipid membrane edge by annexin A5 trimers.

Plasma membrane damage occurs in healthy cells and more frequently in cancer cells where high growth rates and metastasis result in frequent membrane damage. The annexin family of proteins plays a key role in membrane repair. Annexins are recruited at the membrane injury site by Ca and repair the damaged membrane in concert with several other proteins.

Identification of inhibitors targeting the energy-coupling factor (ECF) transporters.

The energy-coupling factor (ECF) transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. The central role of vitamin transport in the metabolism of bacteria and absence from humans make the ECF transporters an attractive target for inhibition with selective chemical probes.

DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.

DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene transcription. Supercoiling affects all scales of the spatio-temporal organization of bacterial DNA, from the base pair to the large scale chromosome conformation.

Dynamics of fluid bilayer vesicles: Soft meshes and robust curvature energy discretization.

Continuum models like the Helfrich Hamiltonian are widely used to describe fluid bilayer vesicles. Here we study the molecular dynamics compatible dynamics of the vertices of two-dimensional meshes representing the bilayer, whose in-plane motion is only weakly constrained. We show (i) that Jülicher's discretization of the curvature energy offers vastly superior robustness for soft meshes compared to the commonly employed expression by Gommper and Kroll and (ii) that for sufficiently soft meshes, the typical behavior of fluid bilayer vesicles can emerge even if the mesh connectivity remains fixed throughout the simulations.

Multiscale equilibration of highly entangled isotropic model polymer melts.

We present a computationally efficient multiscale method for preparing equilibrated, isotropic long-chain model polymer melts. As an application, we generate Kremer-Grest melts of 1000 chains with 200 entanglements and 25 000-2000 beads/chain, which cover the experimentally relevant bending rigidities up to and beyond the limit of the isotropic-nematic transition. In the first step, we employ Monte Carlo simulations of a lattice model to equilibrate the large-scale chain structure above the tube scale while ensuring a spatially homogeneous density distribution.

Earth's volatile depletion trend is consistent with a high-energy Moon-forming impact.

The abundance of volatile elements in the silicate Earth relative to primitive chondrites provides an important constraint on the thermochemical evolution of the planet. However, an overabundance of indium relative to elements with similar nebular condensation temperatures is a source of debate. Here we use ab initio molecular dynamics simulations to explore the vaporization behavior of indium from pyrolite melt at conditions of the early magma ocean just after the Moon-forming impact.

Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas.

Flexibility is essential for many proteins to function, but can be difficult to characterize. Experiments lack resolution in space and time, while the time scales involved are prohibitively long for straightforward molecular dynamics simulations. In this work, we present a multiple state transition path sampling simulation study of a protein that has been notoriously difficult to characterize in its active state.

Equivalence between pressure- and structure-defined ionization in hot dense carbon.

The determination of the ionization of a system in the hot dense regime is a long standing issue. Recent studies have shown inconsistencies between standard predictions using average atom models and evaluations deduced from electronic transport properties computed with quantum molecular dynamics simulations [Bethkenhagen et al., Phys.

Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells.

When human cord blood-derived CD34+ cells are induced to differentiate, they undergo rapid and dynamic morphological and molecular transformations that are critical for fate commitment. In particular, the cells pass through a transitory phase known as "multilineage-primed" state. These cells are characterized by a mixed gene expression profile, different in each cell, with the coexpression of many genes characteristic for concurrent cell lineages.

Diamond formation kinetics in shock-compressed C─H─O samples recorded by small-angle x-ray scattering and x-ray diffraction.

Extreme conditions inside ice giants such as Uranus and Neptune can result in peculiar chemistry and structural transitions, e.g., the precipitation of diamonds or superionic water, as so far experimentally observed only for pure C─H and HO systems, respectively.

The Speciation and Coordination of a Deep Earth Carbonate-Silicate-Metal Melt.

Ab initio molecular dynamics calculations on a carbonate-silicate-metal melt were performed to study speciation and coordination changes as a function of pressure and temperature. We examine in detail the bond abundances of specific element pairs and the distribution of coordination environments over conditions spanning Earth's present-day mantle. Average coordination numbers increase continuously from 4 to 8 for Fe and Mg, from 4 to 6 for Si, and from 2 to 4 for C from 1 to 148 GPa (4,000 K).

Virial expansion of the electrical conductivity of hydrogen plasmas.

The low-density limit of the electrical conductivity σ(n,T) of hydrogen as the simplest ionic plasma is presented as a function of the temperature T and mass density n in the form of a virial expansion of the resistivity. Quantum statistical methods yield exact values for the lowest virial coefficients which serve as a benchmark for analytical approaches to the electrical conductivity as well as for numerical results obtained from density functional theory-based molecular dynamics simulations (DFT-MD) or path-integral Monte Carlo simulations. While these simulations are well suited to calculate σ(n,T) in a wide range of density and temperature, in particular, for the warm dense matter region, they become computationally expensive in the low-density limit, and virial expansions can be utilized to balance this drawback.

Genesis of a CO-rich and HO-depleted atmosphere from Earth's early global magma ocean.

The magma ocean was a important reservoir for Earth’s primary volatiles. Understanding the volatile fluxes between the early atmosphere and the magma ocean is fundamental for quantifying the volatile budget of our planet. Here we investigate the vaporization of carbon and hydrogen at the boundary between the magma ocean and the thick, hot early atmosphere using first-principles molecular dynamics calculations.

Monte Carlo simulation of a lattice model for the dynamics of randomly branching double-folded ring polymers.

Supercoiled DNA, crumpled interphase chromosomes, and topologically constrained ring polymers often adopt treelike, double-folded, randomly branching configurations. Here we study an elastic lattice model for tightly double-folded ring polymers, which allows for the spontaneous creation and deletion of side branches coupled to a diffusive mass transport, which is local both in space and on the connectivity graph of the tree. We use Monte Carlo simulations to study systems falling into three different universality classes: ideal double-folded rings without excluded volume interactions, self-avoiding double-folded rings, and double-folded rings in the melt state.

Buoyancy and Structure of Volatile-Rich Silicate Melts.

The early Earth was marked by at least one global magma ocean. Melt buoyancy played a major role for its evolution. Here we model the composition of the magma ocean using a six-component pyrolite melt, to which we add volatiles in the form of carbon as molecular CO or CO and hydrogen as molecular HO or through substitution for magnesium.

Single-molecule stretching experiments of flexible (wormlike) chain molecules in different ensembles: Theory and a potential application of finite chain length effects to nick-counting in DNA.

We propose a formalism for deriving force-elongation and elongation-force relations for flexible chain molecules from analytical expressions for their radial distribution function, which provides insight into the factors controlling the asymptotic behavior and finite chain length corrections. In particular, we apply this formalism to our previously developed interpolation formula for the wormlike chain end-to-end distance distribution. The resulting expression for the asymptotic limit of infinite chain length is of similar quality to the numerical evaluation of Marko and Siggia's variational theory and considerably more precise than their interpolation formula.