arXiv subjects

Iliya D. Stoev

Publications and source records attributed to Iliya D. Stoev.

5 recordsLinked to original sources

arXiv2026

Structural Certification for Reliable Physical Design with Language Models

An unreliable language model can be made to produce reliable physical designs if the authority to assert is moved out of the model: the model proposes, and a deterministic engine alone certifies, returning certified, impossible, or unknown. We introduce Physics-Anchored Certification (PHACT), a propose-certify loop spanning five scientific domains, and identify what makes such a certificate trustworthy. A checker that accepts a model-supplied value can be forged; deriving the certified quantity from fixed inputs instead makes forgery impossible by construction. Across eighty adversarial trials spanning two models, two decoding temperatures, and a deliberately faulted engine, this contract produced zero false certifications.

cs.AI↗

arXiv2026

Synergistic approach to probing the dynamics and mechanics of patchy soft matter

Tailoring microscopic details to tune bulk rheology is a key paradigm in soft matter physics, yet the vast parameter space associated with constituent interactions precludes a fully systematic approach. To address this, we have designed a synergistic strategy to explore the parameter space that comprises simulations, experimental rheology, and machine learning. As a case study, we choose DNA-based self-assembled fluids whose viscoelastic response can be fine-tuned by manipulating the base sequencing of the constituent nucleic acid nanostars. We use coarse-grained simulations, benchmarked against experimental data, to obtain the rheology of the DNA fluids, which feeds forward to a framework of Gaussian Process Regression and active learning. The latter is then used to explore the rheological design space with high predictive precision. The pipeline is designed to be deployed iteratively for the rational design and accelerated discovery of generic soft matter suspensions.

cond-mat.soft↗

arXiv2026

DWS-based microrheology of triblock copolymers

The thermally reversible phase transitions in aqueous solutions of the triblock copolymers known as Pluronic and their related textures are well-researched. However, their corresponding rheological properties are less studied. In particular, their high-temperature behavior is difficult to access with classical rheology. Here we demonstrated that Diffusing Wave Spectroscopy (DWS)-based microrheology allows us to study the phase transition and the associated viscoelastic properties of Pluronic F127 solutions for temperatures from 5 C to 80 C. From the measured intensity-autocorrelation functions we can extract effective viscosities and determine the critical micellization temperature and concentration. Moreover,the high EO/PO (arm-to-core) ratio of F127 and its polydispersity play a critical role in the high-temperature re-entrant liquid phase, due to decreasing solubility of PEO along with the dehydration of the PPO core. The microscopic viscoelastic moduli G'(ω) and G''(ω) help to determine these phase transitions and provide mechanical properties in the solid phase that are not readily accessible with standard multi-particle tracking techniques due to limited Brownian motion.

cond-mat.soft↗

arXiv2020

Inhibiting amyloid-like aggregation through bio-conjugation of proteins with polymer surfactant

Prevention of protein aggregation and thus stabilization of proteins has large biological and biotechnological implications. Here, we show that inhibition of amyloid-like aggregates is possible in stoichiometric conjugates of polymer surfactant and bovine serum albumin (BSA) chosen as a model protein. We investigate using a combination of Thioflavin-T fluorescence spectroscopy, dynamic light scattering and FTIR spectroscopy the aggregation behavior in polymer surfactant modified and unmodified (native) BSA solutions. The BSA-polymer surfactant conjugates are stable up to 5 days under aggregation conditions, while native BSA forms amyloid fibrillar structures. Further, DLS-based micro-rheology studies performed with heat-treated 100 to 200 μM native BSA aggregates provided understanding of the equilibrium elastic and viscous moduli over a very large frequency range, reaching MHz, which are inaccessible using bulk rheology. Our results indicate that after 6 days of aggregation conditions, elastic moduli showed values between 1.2 to 3.6 Pa corresponding to an entanglement length (ξ) of 105 nm. Interestingly, heating 200 μM native BSA solution at 65 degree C for 2 days in a plastic Eppendorf resulted in self-standing films. These films exhibited strong ThT-fluorescence intensity and a predominant \b{eta}-sheet secondary structure from the FTIR studies, suggesting that self-standing microstructure resulted from hierarchical self-assembly of amyloid fibrils.

q-bio.BM↗

arXiv2019

On the Role of Flexibility in Linker-Mediated DNA Hydrogels

Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we use linker-mediated gels, where the sticky ends of two trivalent nanostars are connected through the complementary sticky ends of a linear DNA duplex. We can design this connection to be either rigid or flexible by introducing flexible, non-binding bases. The additional flexiblity provided by these non-binding bases influences the effective elasticity of the percolating gel formed at low temperatures. Here we show that by choosing the right length of the linear duplex and non-binding flexible joints, we obtain a completely different phase behaviour to that observed for rigid linkers. In particular, we use dynamic light scattering as microrheological tool to monitor the self-assembly of DNA nanostars with linear linkers as a function of temperature. While we observe classical gelation when using rigid linkers, the presence of flexible joints leads to a cluster fluid with reduced viscosity. Using both the oxDNA model and a coarse-grained simulation to investigate the nanostar-linker topology, we hypothesise on the possible structure formed by the DNA clusters.

physics.bio-ph↗