Related papers: Chemomechanical simulation of microtubule dynamics…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
We have implemented vibronic dynamics for simulations of the third order coherent response of electronic dimers. In the present communication we provide the full and detailed description of the dynamical model, recently used for simulations…
We investigate the dynamics of an idealized model of microtubule growth that evolves by: (i) attachment of guanosine triphosphate (GTP) at rate lambda, (ii) conversion of GTP to guanosine diphosphate (GDP) at rate 1, and (iii) detachment of…
Electroporation is a complex, iterative, and nonlinear phenomenon that is often studied by numerical simulations. In recent years, tissue electroporation simulations have been performed using static models. However, the results of a static…
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T=3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to…
Active emulsions and liquid crystalline shells are intriguing and experimentally realisable types of topological matter. Here we numerically study the morphology and spatiotemporal dynamics of a double emulsion, where one or two passive…
Design of robots at the small scale is a trial-and-error based process, which is costly and time-consuming. There are few dynamic simulation tools available to accurately predict the motion or performance of untethered microrobots as they…
We use optical trapping to continuously bend an isolated microtubule while simultaneously measuring the applied force and the resulting filament strain, thus allowing us to determine its elastic properties over a wide range of applied…
Different propulsion mechanisms have been suggested for describing the motion of a variety of chemical micromotors, including the bubble-recoil mechanism, which has attracted great attention in the last decades due to its high efficiency…
This review describes the analytical calculation of lateral pressure profile in lipid membrane with finite curvature. The derivation is based on the previously developed microscopic model of flexible strings [1,2]. According to this theory…
This study delves into Microtearing Modes (MTMs) in tokamak plasmas, employing advanced simulations within the BOUT++ framework. The research, centering on collisional MTMs influenced by the time-dependent thermal force, enhances our…
Using molecular dynamics we investigate the thermodynamics, dynamics and structure of 250 diatomic molecules interacting by a core-softened potential. This system exhibits thermodynamics, dynamics and structural anomalies: a maximum in…
Microtubules, major elements of the cell skeleton are, most of the time, well organized in vivo, but they can also show self-organizing behaviors in time and/or space in purified solutions in vitro. Theoretical studies and models based on…
Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate…
We investigate the structural and dynamical properties of binary aluminum-titanium liquid metallic alloys, as a function of temperature and composition. We make use of MD-simulations, using a transferable machine-learning potential…
Active turbulence is a paradigmatic and fascinating example of self-organized motion at large scales occurring in active matter. We employ massive hydrodynamic simulations of suspensions of resolved model microswimmers to tackle the…
We investigate the dynamics of an active gel of bundled microtubules that is driven by clusters of kinesin molecular motors. Upon the addition of ATP, the coordinated action of thousands of molecular motors drives the gel to a highly…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…
Understanding the mechanisms responsible for the formation and growth of FtsZ polymers and their subsequent formation of the $Z$-ring is important for gaining insight into the cell division in prokaryotic cells. In this work, we present a…