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Transporting between arbitrary distributions is a fundamental goal in generative modeling. Recently proposed diffusion bridge models provide a potential solution, but they rely on a joint distribution that is difficult to obtain in…
Understanding frictional phenomena is a fascinating fundamental problem with huge potential impact on energy saving. Such an understanding requires monitoring what happens at the sliding buried interface, which is almost inaccessible by…
A novel numerical formulation for solving fluid-structure interaction (FSI) problems is proposed where the fluid field is spatially discretized using smoothed particle hydrodynamics (SPH) and the structural field using the finite element…
The interaction of screw dislocations with an applied stress is studied using atomistic simulations in conjunction with a continuum treatment of the role played by the far field boundary condition. A finite cell of atoms is used to consider…
Boundary element methods (BEM) reduce a partial differential equation in a domain to an integral equation on the domain's boundary. They are particularly attractive for solving problems on unbounded domains, but handling the dense matrices…
In contact mechanics computation, the constraint conditions on the contact surfaces are typically enforced by the Lagrange multiplier method, resulting in a saddle point system. The mortar finite element method is usually employed to…
Numerical solutions to fractional differential equations can be extremely computationally intensive due to the effect of non-local derivatives in which all previous time points contribute to the current iteration. In finite difference…
Specific molecular interactions underlie unexpected and useful phenomena in nanofluidic systems, but require descriptions that go beyond traditional macroscopic hydrodynamics. In this letter, we demonstrate how equilibrium molecular…
Cell blebs are protrusions of the cell membrane and can be instrumental for cell migration. We derive a continuum model for the mechanical and geometrical aspects of the onset of blebbing in terms of a force balance. It is abstract and…
We present a barrier method for treating frictional contact on interfaces embedded in finite elements. The barrier treatment has several attractive features, including: (i) it does not introduce any additional degrees of freedom or…
Response of lipid bilayers to external mechanical stimuli is an active area of research with implications for fundamental and synthetic cell biology. However, there is a lack of tools for systematically imposing mechanical strains and…
In the following work we apply the boundary element method to two-phase flows in shallow microchannels, where one phase is dispersed and does not wet the channel walls. These kinds of flows are often encountered in microfluidic…
We investigate the dynamics of a phase-separating binary fluid, containing colloidal dumbbells anchored to the fluid-fluid interface. Extensive Lattice Boltzmann-Immersed Boundary method simulations reveal that the presence of soft…
We report on salt-dependent interaction potentials of a single charged particle suspended in a binary liquid mixture above a charged wall. For symmetric boundary conditions (BC) we observe attractive particle-wall interaction forces which…
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+)…
In our recent work [H. Zhang, F.X. Trias, A. Oliva, D. Yang, Y. Tan, Y. Sheng. PIBM: Particulate immersed boundary method for fluid-particle interaction problems. Powder Technology. 272(2015), 1-13.], a particulate immersed boundary method…
The immersed boundary (IB) method is a mathematical and numerical framework for problems of fluid-structure interaction, treating the particular case in which an elastic structure is immersed in a viscous incompressible fluid. The IB…
Continuum or discrete polarizable models for the study of optoelectronic processes in embedded subsystems rely mostly on the restriction of the surrounding electronic dielectric response to its low frequency limit. Such a description hinges…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong…