Network inference methods are widely used to study regulatory interplay in biological systems. Such methods are usually based on simple, often linear, approximations to underlying dynamics. We present a network inference methodology that is rooted in nonlinear biochemical kinetics. This is done by considering a dynamical system that depends on a reaction graph, summarizing all biochemical react...

where x is a vector of displacements of structural coordinates, M is a positive definite mass matrix, C is a non-negative definite damping matrix, and K is a non-negative definite stiffness matrix. The nonlinear restoring forces are given in R(x, ẋ) and f ext(t) is a vector of external dynamic loads. At any point in time, t = ti+1 = (i+ 1)h, we may solve for the accelerations in terms of the di...

Protein synthesis is inherently a dynamic process, requiring both small-scale and large-scale movements of tRNA and mRNA. It has long been suspected that these movements might be coupled to conformational changes in the ribosome, and in its RNA moieties in particular. Recently, the nature of ribosome structural dynamics has begun to emerge from a combination of approaches, most notably cryo-EM,...

A critical study of the process necessary to create structural control models is made. Exact closed-form solutions of beams and truss-beams continuous models open and closed loop dynamics are given, and used to evaluate the low frequency accuracy of hand prefined finite element models. For trusses condensed models and refined joint behavior are considered, using the equivalent continuum approac...

The structural dynamics of graphite and graphene are unique, because of the selective coupling between electron and lattice motions and hence the limit on electric and electro-optic properties. Here, we report on the femtosecond probing of graphite films (1–3 nm) using ultrafast electron crystallography in the transmission mode. Two time scales are observed for the dynamics: a 700 fs initial de...

The communication of structure in musical expression has been studied scientifically by analyzing variations in timing and dynamics in expert performances, and by analysis by synthesis. The underlying principles have been extracted, and models of the relationship between expression and musical structure formulated. For example, a musical phrase tends to speed up and get louder at the start, and...

We review our recent time- and angle-resolved photoemission spectroscopy experiments, which measure the transient electronic structure of optically driven graphene. For pump photon energies in the near infrared ([Formula: see text]), we have discovered the formation of a population-inverted state near the Dirac point, which may be of interest for the design of THz lasing devices and optical amp...