Related papers: Mesoscale computational protocols for the design o…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
The microscopic structure of several amorphous substances often reveals complex patterns such as medium- or long-range order, spatial heterogeneity, and even local polycrystallinity. To capture all these features, models usually incorporate…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
Micelles and vesicles are promising candidates in targeted drug/gene delivery, bioreactors, and templates for nanoparticle synthesis. We investigated the morphology and dynamics of PEG-PDMS-PEG triblock copolymer nano-scale assemblies…
The dynamics of compressible liquid-vapor flow depends sensitively on the microscale behavior at the phase boundary. We consider a sharp-interface approach, and propose a multiscale model to describe liquid-vapor flow accurately, without…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
The dynamics of a self-propelled particle are typically hard-wired by its microscopic construction, limiting the range of behaviors accessible without redesigning the particle itself. Here we show that intramolecular nonreciprocity provides…
The structural and thermodynamic properties of mixtures of colloidal spheres and non-adsorbing polymer chains are studied within a novel general two-component macromolecular liquid state approach applicable for all size asymmetry ratios.…
We investigate effective interactions between a colloidal particle, immersed in a binary mixture of smaller spheres, and a semipermeable membrane. The colloid is modeled as a big hard sphere and the membrane is represented as an infinitely…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Healthcare applications are inherently multimodal, benefiting greatly from the integration of diverse data sources. However, the modalities available in clinical settings can vary across different locations and patients. A key area that…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
With the rise of service-oriented computing, applications are more and more based on coordination of autonomous services. Envisioned over largely distributed and highly dynamic platforms, expressing this coordination calls for alternative…
Nucleic acids physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse grained models, e.g. the worm-like-chain, taken from polymer physics. In this article, I present an…
Complex fluid-fluid interfaces featuring mesoscale structures with adsorbed particles are key components of newly designed materials which are continuously enriching the field of soft matter. Simulation tools which are able to cope with the…
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…
A multicompartment mathematical model is presented with the goal of studying the role of dose-dense protocols in the context of combination cancer chemotherapy. Dose-dense protocols aim at reducing the period between courses of chemotherapy…
The paper analyzes theoretically the influence of fullerenes on the characteristics of $\mathrm{Al/C}_{60}$ composites. The molecular dynamics method is used to study the dependences of density and stiffness constants on the concentration…