We present a computational learning method for bio-molecular classification. This method shows how to design biochemical operations both for learning and pattern classification. As opposed to prior work, our molecular algorithm learns generic classes considering the realization in vitro via a sequence of molecular biological operations on sets of DNA examples. Specifically, hybridization betwee...

The HSP70s belong to a small family of highly conserved ∼70 kDa enzymes that can use the energy of ATP-hydrolysis to modify the structure, and consequently the function, of specific native proteins, and to unfold, solubilize, and thereby reduce the cellular concentration of harmful misfolded proteins (Finka et al., 2016). Particular HSP70s are expressed constitutively in the cytosol of bacteria...

The use of EM and image analysis techniques, particularly the single particle methodology, has opened the door to the structural characterization of large protein complexes in the megadalton range. This review covers the basic principles of single particle EM and recent examples of its application to the study of large molecular machines in the eukaryotic cell. These examples will give the read...

Biologically inspired computation has been recently used with mathematical models towards the design of new synthetic organisms. In this work, we use Pareto optimality to optimize these organisms in a multi-objective fashion. We infer the best knockout strategies to perform specific tasks in bacteria, which involve concurrent maximization/minimization of multiple functions (codomain) and optimi...

Roop Mallik studies how molecular motors and lipids interact to drive intracellular transport.

We could paraphrase Professor Noyori [1] and say that the science of molecular machines is four-dimensional chemistry since their 3D structure (x, y, z) is coupled to their motion and kinetics (t). In condensed phases at equilibrium, the motion is erratic with equal probabilities of moving forward or backward according to the principle of detailed balance. Therefore, unidirectional motion is po...