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We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
Amorphous materials exhibit peculiar mechanical and vibrational properties, including non-affine elastic responses and excess vibrational states, i.e., the so-called boson peak. For polymer glasses, these properties are considered to be…
Polydispersity is a universal feature of synthetic polymers and biological molecules in the cytoplasm. However, its quantitative impact on collective behavior remains poorly understood because conventional metrics, such as the…
Metamaterials are engineered materials composed of specially designed unit cells that exhibit extraordinary properties beyond those of natural materials. Complex engineering tasks often require heterogeneous unit cells to accommodate…
Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have…
Most approaches for designing self-assembled materials focus on the thermodynamic stability of a target structure or crystal polymorph. Yet in practice, the outcome of a self-assembly process is often controlled by kinetic pathways. Here we…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
Generative modeling has become a central paradigm in protein research, extending machine learning beyond structure prediction toward sequence design, backbone generation, inverse folding, and biomolecular interaction modeling. However, the…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
Since the 1920s, packing arguments have been used to rationalize crystal structures in systems ranging from atomic mixtures to colloidal crystals. Packing arguments have recently been applied to complex nanoparticle structures, where they…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
Inspired by protein folding, we explored the construction of three-dimensional structures and machines from one-dimensional chains of simple building blocks. This approach not only allows us to recreate the self-replication mechanism…
We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry.…
We propose a solution strategy for a multimaterial minimum compliance topology optimization problem, which consists in finding the optimal allocation of a finite number of candidate (possibly anisotropic) materials inside a reference…
We clarify the mathematical structure underlying unitary $t$-designs. These are sets of unitary matrices, evenly distributed in the sense that the average of any $t$-th order polynomial over the design equals the average over the entire…
Large sets of combinatorial designs has always been a fascinating topic in design theory. These designs form a partition of the whole space into combinatorial designs with the same parameters. In particular, a large set of block designs,…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…