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Soluble alpha-amylases play an important role in the catabolism of polysaccharides. In this work, we show that the enzyme can interact with the lipid membrane and further alter its mechanical properties. Vesicle fluctuation spectroscopy is…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
In a previous study (Comp. Phys. Com.(2005) Vol.169, 139-143), we clarified the dependence of the phase structure on the hydrophilicity of an amphiphilic molecule by varying the interaction potential between the hydrophilic molecule and…
We consider a rigid assembly of two active Brownian particles, forming an active colloidal dimer, in a gradient of activity. We show analytically that depending on the relative orientation of the two particles the active dimer accumulates…
Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This…
Alzheimer's disease (AD) is marked by the pathological accumulation of amyloid beta-42 (Abeta-42), contributing to synaptic dysfunction and neurodegeneration. While extracellular amyloid plaques are well-studied, increasing evidence…
The dynamics of microphase separation and the orientation of lamellae in diblock copolymers is investigated in terms of a mean-field model. The formation of lamellar structures and their stable states are explored and it is shown that…
We study the important for the experiment features of the effect of the electron shell on alpha decay in the adiabatic approach. The effect is of tenths of a percent or less in magnitude, depending on the transition energy and the atomic…
Molecular dynamics simulations are used to study the phase behavior of linear multiblock copolymers with two types of monomers, A and B, where the length of the polymer blocks $N_{A}$ and $N_{B}$ ($N_{A}=N_{B}=N$), the number of the blocks…
Vitrimers offer a promising sustainable alternative to conventional epoxies due to their recyclability. Vitrimers are covalent adaptive networks where some bonds can break and reform above the vitrimer transition temperature. While this can…
A very stable binding site for the interaction between an pentameric oligothiophene and an amyloid-$\beta$(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an…
Electronic properties of quasi-two-dimensional molecular conductors $X$[Pd(dmit)$_2$]$_2$ are studied theoretically. We construct an effective model based on the fragment molecular orbital scheme developed recently, which can describe the…
Meso-scale simulation of structure formation for AB-dimers in solution W monomers was performed by dissipative particle dynamics (DPD) algorithm. As a simulation model, modified Jury Model was adopted Jury, S. et al. "Simulation of…
Protein aggregates exhibit diverse morphology, exemplified by amyloid fibrils, gel-like structures, and liquid-like condensates. Differences in the morphologies in identical proteins play important functional roles in several diseases.…
Semiflexible polymers in concentrated lyotropic solution are studied within a bead-spring model by molecular dynamics simulations, focusing on the emergence of a smectic A phase and its properties. We systematically vary the density of the…
Based on thermodynamic integration we introduce atoms in molecules (AIM) using the orbital-free framework of alchemical perturbation density functional theory (APDFT). Within APDFT, atomic energies and electron densities in molecules are…
We conduct molecular dynamics simulations of the collision of atomic clusters with a weakly-attractive surface. We focus on an intermediate regime, between soft-landing and fragmentation, where the cluster undergoes deformation on impact…
The conformational and dynamical properties of active Brownian polymers embedded in a fluid depend on the nature of the driving mechanism, e.g., self-propulsion or external actuation of the monomers. Implementations of self-propelled and…
Polymer blends offer an exciting material for various potential applications due to their tunable properties by varying constituting components and their relative composition. Our simulation results unravel an intrinsic relationship between…
A dimer of bound atoms cannot melt, only dissociate. Bulk metals show a well defined first order transition between their solid and liquid phases. The appearance of the melting transition is explored for increasing clusters sizes via the…