We study the Langevin dynamics of the standard random heteropolymer model by mapping the problem to a supersymmetric field theory using the Martin-Siggia-Rose formalism. The resulting model is solved nonperturbatively employing a Gaussian variational approach. In constructing the solution, we assume that the chain is very long and impose the translational invariance which is expected to be present in the bulk of the globule by averaging over the center of mass coordinate. In this way we derive equations of motion for the correlation and response functions C(t,t') and R(t,t'). The order parameters are extracted from the asymptotic behavior of these functions. We find a dynamical phase diagram with frozen (glassy) and melted (ergodic) phases. In the glassy phase the system fails to reach equilibrium and exhibits aging of the type found in p-spin glasses. Within the approximations used in this study, the random heteropolymer model can be mapped to the problem of a manifold in a random potential with power law correlations.
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http://dx.doi.org/10.1103/PhysRevE.64.051910 | DOI Listing |
Angew Chem Int Ed Engl
January 2025
Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Recently, a new class of synthetic methyl methacrylate-based random heteropolymers (MMA-based RHPs) has displayed protein-like properties. Their function appears to be insensitive to the precise sequence. Here, through atomistic molecular dynamics simulation, we show that there are universal protein-like features of MMA-based RHPs that are insensitive to the sequence, and mostly depend on the overall composition.
View Article and Find Full Text PDFJ Am Chem Soc
March 2024
California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States.
Random heteropolymers (RHPs) consisting of three or more comonomers have been routinely used to synthesize functional materials. While increasing the monomer variety diversifies the side-chain chemistry, this substantially expands the sequence space and leads to ensemble-level sequence heterogeneity. Most studies have relied on monomer composition and simulated sequences to design RHPs, but the questions remain unanswered regarding heterogeneities within each RHP ensemble and how closely these simulated sequences reflect the experimental outcomes.
View Article and Find Full Text PDFAdv Mater
May 2024
College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, China.
Developing artificial ion transport systems, which process complicated information and step-wise regulate properties, is essential for deeply comprehending the subtle dynamic behaviors of natural channel proteins (NCPs). Here a photo-controlled logic-gated K channel based on single-chain random heteropolymers containing molecular motors, exhibiting multi-core processor-like properties to step-wise control ion transport is reported. Designed with oxygen, deoxygenation, and different wavelengths of light as input signals, complicated logical circuits comprising "YES", "AND", "OR" and "NOT" gate components are established.
View Article and Find Full Text PDFProteins
May 2024
Laboratório de Biofísica Teórica, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil.
Random energy models (REMs) provide a simple description of the energy landscapes that guide protein folding and evolution. The requirement of a large energy gap between the native structure and unfolded conformations, considered necessary for cooperative, protein-like, folding behavior, indicates that proteins differ markedly from random heteropolymers. It has been suggested, therefore, that natural selection might have acted to choose nonrandom amino acid sequences satisfying this particular condition, implying that a large fraction of possible, unselected random sequences, would not fold to any structure.
View Article and Find Full Text PDFJ Chem Phys
September 2023
Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
The interfacial behavior of macromolecules dictates their intermolecular interactions, which can impact the processing and application of polymers for pharmaceutical and synthetic use. Using molecular dynamics simulations, we observe the evolution of a random heteropolymer in the presence of liquid-liquid interfaces. The system of interest forms single-chain nanoparticles through hydrophobic collapse in water, lacking permanent crosslinks and making their morphology mutable in new environments.
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