Related papers: Effective potentials and electrostatic interaction…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
For many biotechnological applications it would be useful to better understand the effects produced by electric fields on lipid membranes. This review discusses several aspects of the electrostatic properties of a planar lipid membrane with…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…
Can we avoid molecular dynamics simulations to estimate the electrostatic interaction between charged objects separated by a nanometric distance in water? To answer this question, we develop a continuous model for the dielectric properties…
The molecular dynamics method is applied to simulate the recrystallization of an amorphous/crystalline silicon interface. The atomic structure of the amorphous material is constructed with the method of Wooten, Winer, and Weaire. The…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
We derived free energy functional of a bilayer lipid membrane from the first principles of elasticity theory. The model explicitly includes position-dependent mutual slide of monolayers and bending deformation. Our free energy functional of…
Biomembranes consisting of two opposing phospholipid monolayers, which comprise the so-called lipid bilayer, are largely responsible for the dual solid-fluid behavior of individual cells and viruses. Quantifying the mechanical…
Lipid bilayers forming biological membranes are known to behave as viscous 2D fluids on submicrometer scales; usually they contain a large number of active protein inclusions. Recently, it has been shown [Proc. Nat. Acad. Sci. USA 112,…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
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…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific…
Microscopic stress fields are widely used in molecular simulations to understand mechanical behavior. Recently, decomposition methods of multibody forces to central force pairs between the interacting particles have been proposed. Here, we…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Artificial bilayer lipid membranes (BLMs), along with patch-clamped membranes, are frequently used for functional analyses of membrane proteins. In both methods, the electric properties of membranes are characterized by only one parameter,…
Dielectric interfaces are crucial to the behavior of charged membranes, from graphene to synthetic and biological lipid bilayers. Understanding electrolyte behavior near these interfaces remains a challenge, especially in the case of rough…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Computational modeling is usually applied to aid experimental exploration of advanced materials to better understand the fundamental plasticity mechanisms during mechanical testing. In this work, we perform Molecular dynamics (MD)…
Response of lipid bilayers to external mechanical stimuli is an active area of research with implications for fundamental and synthetic cell biology. However, there is a lack of tools for systematically imposing mechanical strains and…