Related papers: Analysis tools for single-monomer measurements of …
For continuous-time linear stochastic dynamical systems driven by Wiener processes, we consider the problem of designing ensemble filters when the observation process is randomly time-sampled. We propose a continuous-discrete McKean--Vlasov…
We consider the sequential sampling of species, where observed samples are classified into the species they belong to. We are particularly interested in studying some quantities describing the sampling process when there is a new species…
We recently presented a new "artificial intelligence" method for the analysis of high-resolution absorption spectra (Bainbridge and Webb, Mon. Not. R. Astron. Soc. 2017, 468,1639-1670). This new method unifies three established numerical…
This study investigates the crystallization and self-assembly phenomena of polyacrylamide (PAM) solutions during evaporation. While traditional thin-film fabrication methods such as spin coating and drop casting are commonly used, this…
The transition from petascale to exascale computers is characterized by substantial changes in the computer architectures and technologies. The research community relying on computational simulations is being forced to revisit the…
Long reads produced by third-generation sequencing technologies are used to construct an assembly (i.e., the subject's genome), which is further used in downstream genome analysis. Unfortunately, long reads have high sequencing error rates…
A semi-grand-canonical Monte Carlo algorithm is employed in conjunction with the bond fluctuation model to investigate the critical properties of an asymmetric binary (AB) polymer mixture. By applying the equal peak-weight criterion to the…
Single-molecule experimental techniques track the real-time dynamics of molecules by recording a small number of experimental observables. Following these observables provides a coarse-grained, low-dimensional representation of the…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
The stochastic simulation algorithm (SSA) and the corresponding Monte Carlo (MC) method are among the most common approaches for studying stochastic processes. They rely on knowledge of interevent probability density functions (PDFs) and on…
We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…
Ring-shaped deposits can be often found after a droplet evaporates on a substrate. If the fluid in the droplet is a pure liquid and its contact line remains pinned during the process, the mechanism behind such ring-shaped deposition is the…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
Path sampling allows the study of rare events like chemical reactions, nucleation and protein folding via a Monte Carlo (MC) exploration in path space. Instead of configuration points, this method samples short molecular dynamics (MD)…
Capsids of many viruses assemble around nucleic acids or other polymers. Understanding how the properties of the packaged polymer affect the assembly process could promote biomedical efforts to prevent viral assembly or nanomaterials…
The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…
While nucleic-acids can be readily amplified for single-marker detection, a comparable method for proteins assay is currently unavailable. Proteins potentiometric detections at 10-20 molar have been demonstrated, but the mechanism remains…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Atomic force microscopy (AFM) is one of the most promising methods for investigating the structure of materials at the micro and nanoscale levels, as well as their local physical-mechanical properties. The experimental data obtained with…
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of…