Related papers: Synchronized Pivots
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
An analytical method to compute thermodynamic properties of a given Hamiltonian system is proposed. This method combines ideas of both dynamical systems and ensemble approaches to thermodynamics, providing de facto a possible alternative to…
Understanding the adsorption and physical characteristics of supported lipid membranes is crucial for their effective use as model cell membranes. Their morphological and thermodynamic properties at the nanoscale have traditionally been…
We propose the use of microcanonical analyses for numerical studies of peptide aggregation transitions. Performing multicanonical Monte Carlo simulations of a simple hydrophobic-polar continuum model for interacting heteropolymers of finite…
Accurate prediction of antibody-binding sites (epitopes) on antigens is crucial for vaccine design, immunodiagnostics, therapeutic antibody development, antibody engineering, research into autoimmune and allergic diseases, and advancing our…
Comprehensive understanding of particle motion in microfluidic devices is essential to unlock novel technologies for shape-based separation and sorting of microparticles like microplastics, cells and crystal polymorphs. Such particles…
We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
In the present work, we discuss how the functional form of thermodynamic observables can be deduced from the geometric properties of subsets of phase space. The geometric quantities taken into account are mainly extrinsic curvatures of the…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
We consider a model of bilayer lipid membrane with interdigitation, in which the lipid tails of the opposite monolayers interpenetrate. The interdigitation is modeled by linking tails of the hydrophobic chains in the opposite monolayers…
Adaptive humoral immunity, from the physical perspective, can be regarded as the self-organization of the binding energy landscape of antibodies. In biological terms, the humoral immune system evolves and adapts its repertoire of antigen…
Thermodynamic scaling explains the dramatic successes of CTP fused human growth proteins as regards lifetime in vivo and enhanced functionality compared to their wild-type analogues, like Biogen. The theory is semi-quantitative and contains…
The Hamiltonian dynamics associated to classical, planar, Heisenberg XY models is investigated for two- and three-dimensional lattices. Besides the conventional signatures of phase transitions, here obtained through time averages of…
Dissipative particle dynamics (DPD) and multi-particle collision (MPC) dynamics are powerful tools to study mesoscale hydrodynamic phenomena accompanied by thermal fluctuations. To understand the advantages of these types of mesoscale…
Synchronization among globally coupled, chaotic map lattices can be related to stable periodic windows in isolated chaotic maps. This relation provides a simple predictive tool for the understanding of complicated behavior in coupled…
In this position paper, we argue that when hypergraphs are used to capture multi-way local relations of data, their resulting topological features describe global behaviour. Consequently, these features capture complex correlations that can…
A new approach to the study of similarity of temperature profiles is presented. It is applicable for any 2-D fluid flow along an isothermal heated (cooled) wall. The approach is based on a simple concept; the area under a set of scaled…
Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…
We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional traps across the thermal crossover from an amorphous solid- to liquid-like behaviors. While static correlations, that…