Related papers: Collective Molecular Dynamics in Proteins and Memb…
In biological settings membranes typically interact locally with other membranes or the extracellular matrix in the exterior, as well as with internal cellular structures such as the cytoskeleton. Characterization of the dynamic properties…
Biological membranes mainly consist of lipids and proteins. While the proteins have many functions as single molecules, the membrane as a whole displays physical properties that cannot be explained on the single molecule level. For example,…
Biological membranes are elastic media in which the presence of a transmembrane protein leads to local bilayer deformation. The energetics of deformation allow two membrane proteins in close proximity to influence each other's equilibrium…
The nucleation of gas hydrates is of great interest in flow assurance, global energy demand, and carbon capture and storage. A complex molecular understanding is critical to control hydrate nucleation and growth in the context of potential…
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon…
Water molecules confined between biological membranes exhibit a distinctive non-Gaussian displacement distribution, far different from bulk water. Here, we introduce a new transport equation for water molecules in the intermembrane space,…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
The paper presents a novel approach to the description of the nonrelativistic weak interaction of a massive neutral particle (lepton) and a nucleus, in which the latter retains its integrity. The cross section of such a process is a sum of…
Membrane curvature sensing is essential for a diverse range of biological processes. Recent experiments have revealed that a single nanometer-sized septin protein can distinguish between membrane-coated glass beads of one micron and three…
Active networks made of biopolymers and motor proteins are valuable bioinspired systems that have been used in the last decades to study the cytoskeleton and its self-organization under mechanical stimulation. Different techniques are…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation, the membrane bends at the point of…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
Machine learning has emerged as a powerful tool in materials discovery, enabling the rapid design of novel materials with tailored properties for countless applications, including in the context of energy and sustainability. To ensure the…
We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow…
An analysis on the discrete versus continuous views of kinetics of macromolecules is presented. It is shown that the discrete approach traditional to biochemistry is insufficient for understanding the dynamics of protein molecules in…
Using numerical simulations, we characterized the behavior of an elastic membrane immersed in an active fluid. Our findings reveal a nontrivial folding and re-expansion of the membrane that is controlled by the interplay of its resistance…
We recently introduced a wave-mechanical model for quasi-elastic neutron scattering (QENS) in proteins. We call the model ELM for "Energy Landscape Model". We postulate that the spectrum of the scattered neutrons consists of lines of…
In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…