Biology subjects

Akram, S. A.

Publications and source records attributed to Akram, S. A..

3 recordsLinked to original sources

bioRxiv2026

Linker stretching optimizes bonding entropy in sticker-spacer condensates

Phase separating biopolymers are often described by the sticker-spacer model, which accounts for non-attractive linkers that connect discrete attractive moieties. "Associative polymer" theories describe these systems as two coexisting fluids of stickers and spacers, respectively. In such theories the stickers and spacers are decoupled in the sense that sticker binding does not affect spacer conformations or vice versa. Informed by coarse-grained simulations, we develop a phenomenological mean-field theory to determine the microscopic coupling between the sticker and spacer degrees of freedom. Accounting for linkers connecting adjacent spacers introduces free energy contributions due to conformational entropy of the spacer and the binding combinatorics of the stickers. These contributions have opposite dependencies on spacer length because longer spacers allow a greater volume to search for binding partners but incur a greater entropy cost upon bond formation. The length dependent terms from these contributions cancel leaving a length-independent elastic term arising from the fact that a small amount of spacer stretching lowers the free energy by increasing the number of possible binding partners. The cancellation of spacer length from the theory justifies the decoupling approximation and supports mean-field treatments of heterogeneous spacers.

biophysics↗

bioRxiv2025

Biomolecular phase boundaries are described by a solubility product that accounts for variable stoichiometry and soluble oligomers

The solubility product is a rigorous description of the phase boundary for salt precipitation and has previously been shown to qualitatively describe the condensation of biomolecules. Here we present a derivation of the solubility product showing that the solubility product is also a robust description of biomolecule phase boundaries if care is taken to account for soluble oligomers and variable composition within the dense phase. Our calculation describes equilibrium between unbound monomers, the dense phase, and an ensemble of oligomer complexes with significant finite-size contributions to their free energy. The biomolecule phase boundary very nearly resembles the power law predicted by the solubility product when plotted as a function of the monomer concentrations. However, this simple form is concealed by the presence of oligomers in the dilute phase. Accounting for the oligomer ensemble introduces complexities to the power law phase boundary including re-entrant behavior and large shifts for stoichiometrically matched molecules. We show that allowing variable stoichiometry in the dense phase expands the two phase region, which appears as curvature of the phase boundary on a double-logarithmic plot. Furthermore, this curvature can be used to predict variations in the dense phase composition at different points along the phase boundary. Finally, we show how the solubility product power law can be identified in experiments by using dilute phase dissociation constants to account for the oligomer ensemble.

biophysics↗

bioRxiv2021

Deformation of membrane vesicles due to chiral surface proteins

Chiral, rod-like molecules can self-assemble into cylindrical membrane tubules and helical ribbons. They have been successfully modeled using the theory of chiral nematics. Models have also predicted the role of chiral lipids in forming nanometer-sized membrane buds in the cell. However, in most theoretical studies, the membrane shapes are considered fixed (cylinder, sphere, saddle, etc.), and their optimum radius of curvatures are found variationally by minimizing the energy of the composite system consisting of membrane and chiral nematics. Numerical simulations have only recently started to consider membrane deformation and chiral orientation simultaneously. Here we examine how deformable, closed membrane vesicles and chiral nematic rods mutually influence each others shape and orientation, respectively, using Monte-Carlo (MC) simulation on a closed triangulated surface. For this, we adopt a discrete form of chiral interaction between rods, originally proposed by Van der Meer et al. (1976) for off-lattice simulations. In our simulation, both conical and short cylindrical tubules emerge, depending on the strength of the chiral interaction and the intrinsic chirality of the molecules. We show that the Helfrich-Prost term, which couple nematic tilt with local membrane curvature in continuum models, can account for most of the observations in the simulation. At higher chirality, our theory also predicts chiral tweed phase on cones, with varying bandwidths. PACS numbers: PACS : 87.16.-b, 87.15.Aa, 81.40.Jj, 87.15.Rn

biophysics↗