Essays about: "molecular simulation"

Showing result 1 - 5 of 68 essays containing the words molecular simulation.

  1. 1. Simulated molecular adder circuits on a surface of DNA : Studying the scalability of surface chemical reaction network digital logic circuits

    University essay from KTH/Skolan för elektroteknik och datavetenskap (EECS)

    Author : Jakob Arvidsson; [2023]
    Keywords : Surface chemical reaction networks; Molecular computing; DNA computing; Circuit simulation; Adders; Ytbundna kemiska reaktionsnätverk; Molekylär beräkning; DNA-beräkning; Kretssimulering; Additionskretsar;

    Abstract : The behavior of the Deoxyribonucleic Acid (DNA) molecule can be exploited to perform useful computation. It can also be ”programmed” using the language of Chemical Reaction Networks (CRNs). One specialized CRN construct is the Surface Chemical Reaction Network (SCRN). READ MORE

  3. 2. Determining Protein Conformational Ensembles by Combining Machine Learning and SAXS

    University essay from KTH/Tillämpad fysik

    Author : Samuel Eriksson Lidbrink; [2023]
    Keywords : AlphaFold; AlphaFold2; SAXS; protein conformational ensembles; machine learning; protein conformations; reweighting; SAXS; AlphaFold; AlphaFold2; proteinkonformationsensembler; maskininlärning; proteinkonformationer; omviktning;

    Abstract : In structural biology, immense effort has been put into discovering functionally relevant atomic resolution protein structures. Still, most experimental, computational and machine learning-based methods alone struggle to capture all the functionally relevant states of many proteins without very involved and system-specific techniques. READ MORE

  4. 3. Identifying effects of adrenaline and dopamine binding on the beta2-adrenergic receptor structure and function using machine learning

    University essay from KTH/Skolan för teknikvetenskap (SCI)

    Author : Joar Gunnarsson; Leon Bergner; [2023]
    Keywords : beta2-adrenergic receptor; GPCR; adrenaline; dopamine; Machine learning; Molecular dynamics simulation;

    Abstract : The beta2-adrenergic receptor is a G-protein coupled receptor, involved in several physiological processes, which enables signaling through the cell membrane. To study the effect of dopamine and adrenaline binding on the receptor structure and function, we used machine learning methods applied to data from molecular dynamics simulations. READ MORE

  5. 4. Accelerating a Molecular Docking Application by Leveraging Modern Heterogeneous Computing Systems

    University essay from KTH/Skolan för elektroteknik och datavetenskap (EECS)

    Author : Gabin Schieffer; [2023]
    Keywords : Molecular docking; AutoDock; GPU; Tensor Core; Drug Discovery; Molekylär dockning; AutoDock; GPU; Tensor Core; Läkemedelsutveckling;

    Abstract : In drug development, molecular docking methods aim at characterizing the binding of a drug-like molecule to a protein. In a typical drug development process, a docking task is repeated millions of time, which makes optimization efforts essential. READ MORE

  6. 5. Comparison and optimization of extracellular vesicle (EV) capturing on functional thin films for their molecular profiling

    University essay from KTH/Tillämpad fysik

    Author : Prattakorn Metem; [2023]
    Keywords : extracellular vesicle; plasmonic nanohole array; atomic force microscopy; fluorescence analysis; extracellulära vesiklar; nanohålsuppsättning; atomkraftsmikroskopi; fluorescensanalys;

    Abstract : Extracellular vesicles (EVs) are lipid bilayer encapsulated nanoparticles which have emerged as an excellent source of biomarkers for multiple diseases, including cancer. However, they are highly heterogeneous in their molecular compositions which remains a major challenge hindering the utilization of their biomarker potential. READ MORE