Phase Separation in Peptide Aggregation Processes - Multicanonical Study of a Mesoscopic Model

We have performed multicanonical computer simulations of a small system of short protein-like heteropolymers and found that their aggregation transition possesses similarities to first-order phase separation processes. Not being a phase transition in the thermodynamic sense, the observed folding-binding behavior exhibits fascinating features leading to the conclusion that the temperature is no suitable control parameter in the transition region. More formally, for such small systems the microcanonical interpretation is more favorable than the typically used canonical picture.Comment: 3 pages, 1 figur

Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat

We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis. Our extension includes the damping of the perpendicular components of the relative velocity, yet keeping the advantages of conserving Galilei invariance and within our error bar also hydrodynamics. This leads to a second friction parameter for tuning the transport properties of the system. Numerical simulations of a simple Lennard-Jones fluid and liquid water demonstrate a very sensitive behaviour of the transport properties, e.g., viscosity, on the strength of the new friction parameter. We envisage that the new thermostat will be very useful for the coarse-grained and adaptive resolution simulations of soft matter, where the diffusion constants and viscosity of the coarse-grained models are typically too high/low, respectively, compared to all-atom simulations.Comment: 6 pages, 4 figure

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach which is a combination of an heterogeneity sensitive spatial domain decomposition with an \textit{a priori} rearrangement of subdomain-walls. Within this approach, the theoretical modeling and scaling-laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase separated binary Lennard-Jones fluid.Comment: 14 pages, 12 figure

Thermodynamics of Peptide Aggregation Processes. An Analysis from Perspectives of Three Statistical Ensembles

We employ a mesoscopic model for studying aggregation processes of protein-like hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase separation process, in which the microcanonical entropy exhibits a convex intruder due to nonnegligible surface effects of the small systems. We analyze thermodynamic properties of the conformational transitions accompanying the aggregation process from the multicanonical, canonical, and microcanonical perspective. It turns out that the microcanonical description is particularly advantageous as it allows for unraveling details of the phase-separation transition in the thermodynamic region, where the temperature is not a suitable external control parameter anymore.Comment: 10 pages, 8 figure

Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir

For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions

C−\mathcal {C}-IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion ($\mathcal {C}-$IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. Additionally, we observe much faster convergence within $\mathcal {C}-$IBI compared to IBI. To validate the robustness, we apply $\mathcal {C}-$IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea

Hierarchies in Nucleation Transitions

We discuss the hierarchy of subphase transitions in first-order-like nucleation processes for an exemplified aggregation transition of heteropolymers. We perform an analysis of the microcanonical entropy, i.e., the density of states is considered as the central statistical system quantity since it connects system-specific entropic and energetic information in a natural and unique way.Comment: 15 pages, 3 figures, Proceedings of the Computational Physics Conference CCP 2010, Jun 23-27, 2010, Trondheim, Norwa