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Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matters in difference phases. Normally, the atomic dynamics are described by classical equations of motion…
Designing robots capable of traversing uneven terrain and overcoming physical obstacles has been a longstanding challenge in the field of robotics. Walking robots show promise in this regard due to their agility, redundant DOFs and…
We study the dynamics of a polymer, described as a variant of a Rouse chain, driven by an active terminal monomer (head). The local active force induces a transition from a globule-like to an elongated state, as revealed by the study of the…
Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecule due to the intricate interplay between their activity and topological constraints. This study focuses on…
Path reweighting is a principally exact method to estimate dynamic properties from biased simulations - provided that the path probability ratio matches the stochastic integrator used in the simulation. Previously reported path probability…
Most passivity based trajectory tracking algorithms for mechanical systems can only stabilise reference trajectories that have constant energy. This paper overcomes this limitation by deriving a single variable Hamiltonian model for the…
Achieving highly dynamic behaviors on humanoid robots, such as running, requires controllers that are both robust and precise, and hence difficult to design. Classical control methods offer valuable insight into how such systems can…
The rate of a chemical reaction can often be determined by the properties of a rank-1 saddle and the associated transition state separating reactants and products. We have found evidence that such rates can be controlled and even enhanced…
We present the exact solutions of various directed walk models of polymers confined to a slit and interacting with the walls of the slit via an attractive potential. We consider three geometric constraints on the ends of the polymer and…
We study the Langevin dynamics of a heteropolymer by means of a mode-coupling approximation scheme, giving rise to a set of coupled integro-differential equations relating the response and correlation functions. The analysis shows that…
Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual…
Legged robot locomotion requires the planning of stable reference trajectories, especially while traversing uneven terrain. The proposed trajectory optimization framework is capable of generating dynamically stable base and footstep…
Predicting the macroscopic mechanical behavior of polymeric materials from the micro-structural features has remained a challenge for decades. Existing theoretical models often fail to accurately capture the experimental data, due to…
Recently there has been remarkable progress in the complex Langevin method, which aims at solving the complex action problem by complexifying the dynamical variables in the original path integral. In particular, a new technique called the…
For reproducing the anomalous -- i.e., sub- or super-diffusive -- behavior in some stochastic dynamical systems, the Generalized Langevin Equation (GLE) has gained considerable popularity in recent years. Motivated by the question whether…
Path integrals with complex actions are encountered for many physical systems ranging from spin- or mass-imbalanced atomic gases and graphene to quantum chromo-dynamics at finite density to the non-equilibrium evolution of quantum systems.…
We have used Langevin dynamics to simulate the forced translocation of linked polymer rings through a narrow pore. For fixed size (i.e. fixed number of monomers) the translocation time depends on the link type and on whether the rings are…
Nonlinear dynamical behaviours in engineering applications can be approximated by linear-parameter varying (LPV) representations, but obtaining precise model knowledge to develop a control algorithm is difficult in practice. In this paper,…
We study the dynamics of a polymer when it is quenched from a $\theta$ solvent into a good or bad solvent by means of a Langevin equation. The variation of the radius of gyration is studied as a function of time. For the first stage of…