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In this work we introduce an Autoencoder for molecular conformations. Our proposed model converts the discrete spatial arrangements of atoms in a given molecular graph (conformation) into and from a continuous fixed-sized latent…
We use a lattice model of a ternary mixture containing saturated and unsaturated lipids with cholesterol (Chol), to study the structural properties characterizing the coexistence between the liquid-disordered and liquid-ordered phases.…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets…
Polymer architecture plays critical roles in both bulk rheological properties and microscale macromolecular dynamics in entangled polymer solutions and composites. Ring polymers, in particular, have been the topic of much debate due to the…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Lipid membranes in a physiological context cannot be understood without taking into account their mobile environment. Here, we report on a high energy-resolution neutron backscattering study to investigate slow motions on nanosecond time…
RNA molecules in living cells form what look like liquid droplets formed by liquid/liquid phase separation. But unlike the molecules in conventional phase separating mixtures, RNA molecules are transported by molecular motors that consume…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
A question of considerable interest to cell membrane biology is whether phase segregated domains across an asymmetric bilayer are strongly correlated with each other and whether phase segregation in one leaflet can induce segregation in the…
Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…
Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
Doxorubicin (DOX) is one of the most efficient antitumor drugs employed in numerous cancer therapies. Its incorporation into lipid-based nanocarriers, such as liposomes, improves the drug targeting into tumor cells and reduces drug side…
We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
A construction method for duplex cage structures with icosahedral sym- metry made out of single-stranded DNA molecules is presented and applied to an icosidodecahedral cage. It is shown via a mixture of analytic and computer techniques that…
We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…