https://scholar.dgist.ac.kr/handle/20.500.11750/842 Sat, 04 Apr 2026 07:18:24 GMT 2026-04-04T07:18:24Z https://scholar.dgist.ac.kr/handle/20.500.11750/58964 Title: AT vs GC binding of protamine-template: A microscopic understanding through molecular dynamics and binding free energies Author(s): Mandal, Sandip; Chhetri, Khadka B.; Jang, Yun Hee; Lansac, Yves; Maiti, Prabal K. Abstract: Protamine, an arginine-rich protein, compacts DNA more tightly than histones in somatic cells, yet its sequence-specific binding remains unclear. Using all-atom MD simulations with an arginine-rich short cationic peptide that mimics the protamine characteristics, we discovered distinct sequence preferences: the peptide binds preferentially to GC-rich sequences in the major groove and AT-rich sequences in the minor groove. Our structural analysis reveals that GC-rich binding induces significant DNA bending, narrowing the major groove and enhancing peptide interactions. In contrast, AT-rich minor grooves are more extended and electronegative, allowing better stereochemical fitting with planar and aromatic guanidinium side groups of arginine. However, thymine's methyl group hinders major groove binding, favoring guanine. Thermodynamic free energy calculations, using molecular mechanics based generalized Born surface area and umbrella sampling, confirm stronger peptide affinity for AT-rich minor grooves and GC-rich major grooves. Overall, these findings will enhance our understanding of sequence-specific DNA condensation and compaction in sperm cells. Mon, 30 Jun 2025 15:00:00 GMT https://scholar.dgist.ac.kr/handle/20.500.11750/58964 2025-06-30T15:00:00Z https://scholar.dgist.ac.kr/handle/20.500.11750/58548 Title: Simulated annealing, spin-coating, and poling: in silico fabrication of ferroelectric polyvinylidene fluoride polymers on graphene as a model of a low-energy-consumption switching device Author(s): Jang, Yun Hee; Ryu, Taekhee; Lansac, Yves Abstract: Ferroelectric polyvinylidene fluoride (PVDF), particularly its β-phase crystals with well-aligned all-trans polymer chains and prominent polarization in composites with other organic or inorganic materials, has attracted great attention in various areas of energy harvesting, storage, and saving. However, since the β phase is not the most stable polymorph of PVDF, a simple solution casting at a low temperature produces a PVDF film with a limited β-phase content, low crystallinity, and/or high porosity. Additional thermal, mechanical, and electrical controls such as annealing, stretching, spin-coating, and poling are required to maximize both the β-phase content and crystallinity of the PVDF film. Herein, the amorphous-to-β-phase crystallization achieved by such processes is mimicked in silico at the molecular level, revealing the effect of each process on the quality of the processed film. The content of the β-phase crystal, which is negligible after the simulated annealing beyond the melting temperature (300 K to 500 K and back to 300 K), increases to 80% after the SLLOD simulations at a shear velocity of 5.5 m s−1 (i.e., by the simulated spin coating of approximately 3000-5000 rpm) and increases further to 100% when combined with a high electric field of 0.18 GV m−1 (i.e., by the simulated electric poling). The perfectly polarized dipole moments of such β-phase PVDF thin films, when deposited on graphene, can induce electrostatic doping (i.e., create charge carriers) in the underlying graphene, even in a zero electric field, resolving the zero-bandgap (i.e., no-OFF-state) issues of graphene while maintaining its high carrier mobility and low-power operation. Indeed, the current-voltage (I-V) curves mimicked by non-equilibrium Green's function calculations on a model device of a field-effect transistor show a modulation of the doping level and in turn the conductance of graphene, virtually achieving an ION/IOFF ratio of up to 20, when the orientation of the PVDF polarization is flipped by a bias gate voltage sweep. We envision that such devices can eventually lead to low-power-consumption high-ON/OFF-ratio graphene-channel field-effect transistors and non-volatile memories. © 2025 The Royal Society of Chemistry. Sat, 31 May 2025 15:00:00 GMT https://scholar.dgist.ac.kr/handle/20.500.11750/58548 2025-05-31T15:00:00Z https://scholar.dgist.ac.kr/handle/20.500.11750/58330 Title: Enhanced electrochemical performance through the structural core–shell morphological tuning of δ-MnO2@C@NiSe2 and realization of asymmetry energy storage devices Author(s): Ampasala, Surya Kiran; Kokkiligadda, Samanth; Yun, Tae Gwang; Lansac, Yves; Jang, Yun Hee; Um, Soong Ho Abstract: This study investigates the synthesis and electrochemical performance of a core–shell architecture comprising amorphous carbon-coated NiSe2 as the core and birnessite δ-MnO2 as the shell. Integrating δ-MnO2, known for its high pseudocapacitance, with a conductive carbon interlayer for efficient electron transport and a stable NiSe2 core, enables superior energy storage and charge transfer dynamics. Structural and morphological optimization of the hybrid electrode enhances ion diffusion and charge storage, resulting in outstanding energy and power densities. The optimized MnO2@C@NiSe2 electrode achieves a remarkable areal capacity of 2236.84 µAh cm−2 and a specific capacity of 272.24mAh g−1, while demonstrating excellent cyclic stability with 75.8 % capacity retention over 10,000 cycles. The fabricated hybrid asymmetric device exhibits a specific capacitance of 173.2F g−1 at 5 mA cm−2 and delivers an ultrahigh areal energy density of 213.6 µWh cm−2 at an areal power density of 21,000 µW cm−2. Cycling stability shows a 76 % capacitance retention after 20,000 cycles using an aqueous KOH electrolyte. Additionally, a pouch cell device demonstrates practical applicability by maintaining a stable 3 V output, effectively powering electronic displays and LED arrays. This work highlights the MnO2@C@NiSe2 core–shell hybrid as a promising candidate for high-performance energy storage and real-world device applications. © 2025 Elsevier B.V. Wed, 30 Apr 2025 15:00:00 GMT https://scholar.dgist.ac.kr/handle/20.500.11750/58330 2025-04-30T15:00:00Z https://scholar.dgist.ac.kr/handle/20.500.11750/57805 Title: Temperature dependent thermoelectric transport in PEDOT-PSS conducting polymer: The effect of additives Author(s): Rohmer, Anthony; Lansac, Yves; Jang, Yun Hee; Limelette, Patrice Abstract: We report on both the electrical and thermoelectric transport properties as a function of temperature in poly(3,4-ethylene dioxythiophene) (PEDOT)-poly(styrene sulfonate) conducting polymers for a wide range of dimethyl sulfoxide (DMSO) additives. Whereas an insulating-like electrical behavior is found over the whole temperature range, a metallic-like thermopower is mainly observed. We show that the resistivity appears to be governed by a three-dimensional variable range hopping mechanism due to disordered regions with a decreasing localization temperature T-0 and an increasing scaling factor rho(0) as a function of the DMSO ratio. The correlation between T-0 and rho(0) demonstrates that they are both controlled by the localization length xi(0), which is strongly enhanced by the DMSO in agreement with the morphological evolution of the PEDOT chains with the additive. On the other hand, the high-T positive metallic-like thermopower seems rather unaffected by the additive in contrast to its low-T counterpart, which appears negative below a characteristic temperature T- s w i t c h. By showing that the latter is closely related to the localization temperature, we propose to ascribe this sign switch to the thermoelectric contribution originating from disordered regions, which competes with the metallic ones due to ordered domains. While still controlled by the localization temperature, this negative contribution appears to be consistent with a phonon-drag component with a scaling behavior as T-0 (T - 3). These analyses allow us to discuss the overall temperature dependent thermoelectric properties in a consistent way by considering a heterogeneous structure with both ordered and disordered domains. By relating explicitly the electrical resistivity to the thermopower, our results do not only reconcile these transport coefficients, but they also provide a unified picture of the properties of the conducting polymers. Tue, 31 Dec 2024 15:00:00 GMT https://scholar.dgist.ac.kr/handle/20.500.11750/57805 2024-12-31T15:00:00Z