Related papers: Dynamic transition from $\alpha$-helices to $\beta…
We perform a systematic application of the hybrid particle-field molecular dynamics technique [Milano et al, J. Chem. Phys. 2009, 130, 214106] to study interfacial properties and potential of mean force (PMF) for separating nanoparticles…
An analysis of the glass transition of four materials with similar chemical structures is performed: PET, PEN and two PET/PEN blends (90/10 and 70/30 w/w). During the melt processing of the blends transesterification reactions yield block…
Connecting cell behavior to tissue shape and mechanics is a key challenge in the physics of morphogenesis. Cytoskeletal turnover precludes a fixed reference state, and tensions are actively generated independently of strain; so conventional…
The present paper deals with the analysis of experimental results taking into account mechanisms brought by the bulk elastic energy transformed by the thermodynamic parameters, temperature, magnetic fields, high hydrostatic pressure…
We propose a novel phase-field model to predict elastic microphase separation in polymer gels. To this end, we extend the Cahn-Hilliard free-energy functional to incorporate an elastic strain energy and a coupling term. These contributions…
We propose an improved prediction method of the tertiary structures of $\alpha$-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method allows wide applications because…
I propose a variation of the standard worm--like chain model to account for internal order parameter (helix/coil) fields on the polymer chain. This internal order parameter field influences polymer conformational statistics by locally…
The transport of particles across lipid-bilayer membranes is important for biological cells to exchange information and material with their environment. Large particles often get wrapped by membranes, a process which has been intensively…
We present results for a lattice model of bio-polymers where the type of $\beta$-sheet formation can be controlled by different types of hydrogen bonds depending on the relative orientation of close segments of the polymer. Tuning these…
We study two closely related, nonlinear models of a viscoplastic solid. These models capture essential features of plasticity over a wide range of strain rates and applied stresses. They exhibit inelastic strain relaxation and steady flow…
The behavior of $\alpha$-quartz under hydrostatic and non-hydrostatic high-pressure conditions has been investigated in Molecular Dynamics simulations of silica in order to clarify the role of non-hydrostatic stresses in the amorphization…
We present fully atomistic Molecular Dynamics simulation results on a main-chain polymer, 1,4-Polybutadiene, in the merging region of the $\alpha$- and $beta$-relaxations. A real space analysis reveals the occurrence of localized motions…
Cellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of…
Fluorescence microscopy has led to impressive quantitative models and new insights gained from richer sets of biomedical imagery. However, there is a dearth of rigorous and established bioimaging strategies for modeling spatiotemporal…
The steady sliding state of periodic structures such as charge density waves and flux line lattices is numerically studied based on two and three dimensional driven random field XY models. We focus on the dynamical phase transition between…
Lipid bilayer membranes are the fundamental biological barriers that permit life. The bilayer dynamics largely participates in orchestrating cellular workings and is characterized by substantial stability together with extreme plasticity…
Plastic deformation in solids induced by external shear stress is of huge practical interest. Presence of local crystalline order in polycrystals, consisting of many grains, distinguishes its deformation pattern from that of amorphous…
Protein phase transitions govern numerous diseases, including neurodegenerative disorders such as Parkinson's and Alzheimer's. In Parkinson's disease, distinct species of the protein alpha-synuclein undergo phase transitions from highly…
We show that a flat two dimensional network of connected vertices, when stretched, may deform plastically by producing `pleats'; system spanning linear structures with width comparable to the lattice spacing, where the network overlaps on…
In this paper, phase field models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic…