All Publications

  • Ensuring thermodynamic consistency with invertible coarse-graining. The Journal of chemical physics Chennakesavalu, S., Toomer, D. J., Rotskoff, G. M. 2023; 158 (12): 124126


    Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insights by isolating the essential degrees of freedom that dictate the thermodynamic properties of a complex, condensed-phase system. The reduced complexity of the model typically leads to lower computational costs and more efficient sampling compared with atomistic models. Designing "good" coarse-grained models is an art. Generally, the mapping from fine-grained configurations to coarse-grained configurations itself is not optimized in any way; instead, the energy function associated with the mapped configurations is. In this work, we explore the consequences of optimizing the coarse-grained representation alongside its potential energy function. We use a graph machine learning framework to embed atomic configurations into a low-dimensional space to produce efficient representations of the original molecular system. Because the representation we obtain is no longer directly interpretable as a real-space representation of the atomic coordinates, we also introduce an inversion process and an associated thermodynamic consistency relation that allows us to rigorously sample fine-grained configurations conditioned on the coarse-grained sampling. We show that this technique is robust, recovering the first two moments of the distribution of several observables in proteins such as chignolin and alanine dipeptide.

    View details for DOI 10.1063/5.0141888

    View details for PubMedID 37003724

  • Unified, Geometric Framework for Nonequilibrium Protocol Optimization. Physical review letters Chennakesavalu, S., Rotskoff, G. M. 2023; 130 (10): 107101


    Controlling thermodynamic cycles to minimize the dissipated heat is a long-standing goal in thermodynamics, and more recently, a central challenge in stochastic thermodynamics for nanoscale systems. Here, we introduce a theoretical and computational framework for optimizing nonequilibrium control protocols that can transform a system between two distributions in a minimally dissipative fashion. These protocols optimally transport a system along paths through the space of probability distributions that minimize the dissipative cost of a transformation. Furthermore, we show that the thermodynamic metric-determined via a linear response approach-can be directly derived from the same objective function that is optimized in the optimal transport problem, thus providing a unified perspective on thermodynamic geometries. We investigate this unified geometric framework in two model systems and observe that our procedure for optimizing control protocols is robust beyond linear response.

    View details for DOI 10.1103/PhysRevLett.130.107101

    View details for PubMedID 36962015

  • Probing the theoretical and computational limits of dissipative design. The Journal of chemical physics Chennakesavalu, S., Rotskoff, G. M. 2021; 155 (19): 194114


    Self-assembly, the process by which interacting components form well-defined and often intricate structures, is typically thought of as a spontaneous process arising from equilibrium dynamics. When a system is driven by external nonequilibrium forces, states statistically inaccessible to the equilibrium dynamics can arise, a process sometimes termed direct self-assembly. However, if we fix a given target state and a set of external control variables, it is not well-understood (i) how to designa protocol to drive the system toward the desired state nor (ii) the cost of persistently perturbing the stationary distribution. In this work, we derive a bound that relates the proximity to the chosen target with the dissipation associated with the external drive, showing that high-dimensional external control can guide systems toward target distribution but with an inevitable cost. Remarkably, the bound holds arbitrarily far from equilibrium. Second, we investigate the performance of deep reinforcement learning algorithms and provide evidence for the realizability of complex protocols that stabilize otherwise inaccessible states of matter.

    View details for DOI 10.1063/5.0067695

    View details for PubMedID 34800948

  • Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators CELL REPORTS Reyer, M. A., Chennakesavalu, S., Heideman, E. M., Ma, X., Bujnowska, M., Hong, L., Dinner, A. R., Vanderpool, C. K., Fei, J. 2021; 36 (13): 109764


    Small RNAs (sRNAs) are important gene regulators in bacteria. Many sRNAs act post-transcriptionally by affecting translation and degradation of the target mRNAs upon base-pairing interactions. Here we present a general approach combining imaging and mathematical modeling to determine kinetic parameters at different levels of sRNA-mediated gene regulation that contribute to overall regulation efficacy. Our data reveal that certain sRNAs previously characterized as post-transcriptional regulators can regulate some targets co-transcriptionally, leading to a revised model that sRNA-mediated regulation can occur early in an mRNA's lifetime, as soon as the sRNA binding site is transcribed. This co-transcriptional regulation is likely mediated by Rho-dependent termination when transcription-coupled translation is reduced upon sRNA binding. Our data also reveal several important kinetic steps that contribute to the differential regulation of mRNA targets by an sRNA. Particularly, binding of sRNA to the target mRNA may dictate the regulation hierarchy observed within an sRNA regulon.

    View details for DOI 10.1016/j.celrep.2021.109764

    View details for Web of Science ID 000704199700015

    View details for PubMedID 34592145