Staff Scientist - Laboratory Of Dr. Dmitry Lyumkis

We are seeking a highly motivated and skilled Staff Scientist to join our dynamic research team focused on deciphering pathways and mechanisms of drug resistance to modern therapies within the Human Immunodeficiency Virus (HIV). The Staff Scientist will develop and implement diverse types of computational experiments, including but not limited to quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics (MD) simulations, free energy perturbation simulations, and novel machine-learning based approaches to investigate pairwise and higher-order residue interactions, with a broad goal of understanding mechanisms of drug resistance in HIV. The Staff Scientist will work with an interdisciplinary team of investigators, whose goal is to understand the structural and mechanistic principles of drug resistance to modern therapies used to treat HIV-infected individuals, and to develop novel therapies that specifically target drug resistant viral variants. The successful candidate will play a crucial role in advancing our understanding of complex biological and chemical systems through computational modeling and simulation techniques. This position offers an excellent opportunity for an individual with a strong background in computational modeling of complex biological phenomena, best practices of quantum mechanical simulations of protein dynamics, and advanced-sampling based molecular simulations to contribute to cutting-edge research projects.
DUTIES AND RESPONSIBILITIES:

• Shape and implement computational strategies to support innovative modality-agnostic design of new drugs against HIV/AIDS resistant strains.
• Design therapeutic molecules and predict their properties using state-of-the-art methodologies integrating chemical, biological and structural data, cheminformatics, and artificial intelligence/machine learning techniques.
• Serve as a scientific expert with both internal and external partners, and provide recommendations regarding targets and emerging external opportunities.
• Use quantum mechanical / molecular mechanical (QM/MM) forcefields and perform free energy perturbation simulations to determine how binding affinities in diverse small molecule ligands change when mutations are introduced into the viral protein assemblies.
• Develop and optimize molecular models and force fields to accurately represent the interactions within the simulated systems.
• Analyze simulation data to extract meaningful insights into the structural and dynamic properties of the studied systems, with extensions to small molecule ligands.
• Develop computational workflows to analyze energetic properties of diverse small molecule inhibitors, with an overall goal of guiding the design of next-gen inhibitors.
• Design and implement simulation protocols, ensuring the validity and relevance of simulations to answer specific questions.
• Utilize and, if necessary, contribute to existing molecular dynamics simulation software packages. Stay informed about the latest developments in simulation methodologies.
• Collaborate with interdisciplinary team of postdoctoral associates, graduate students, and research technicians to provide expertise in molecular dynamics simulations and contribute to the integration of computational results with experimental data.
• Maintain accurate and detailed records of simulation protocols, methodologies, and results. Prepare and present research findings through reports, publications, reviews, and presentations.
• Assist the PI in the development of research grant proposals.
• Performs other related duties as assigned by the PI.

SUPERVISORY RESPONSIBILITIES:

• This job has no supervisory responsibilities.

QUALIFICATIONS:

• Doctoral Degree (Ph.D.) in a related field required.
• Ph.D. in Computational Chemistry, Biophysics, Physics, or a related field preferred.
• Minimum 4 years' post-PhD/MD research experience required.
• Strong background in molecular dynamics simulations with experience in applying various simulation techniques required.
• Familiarity with multiple standard multiscale computational simulation package (e.g., may include Schrodinger suite, MOE/Chemical Computing Group, GROMACS, NAMD) required.
• Experience with multiple therapeutic modalities (e.g. small molecules, biologics, peptides) is strongly preferred.
• Experience working in a cross-functional environment mentoring scientists, influencing decisions and actively setting up and maintaining collaborations is required.
• Experience in scripting computational workflows in Knime, Python or Jupyter notebooks is preferred.
• Effective communication skills, including the ability to present complex scientific concepts to both technical and non-technical audiences.
• Strong track record of creative scientific contributions, including peer reviewed first author publications, patent applications, presentations at national meetings is required.

SALK VALUES:

• Integrity - Guides our moral compass and underpins our every action. We do what is right in all situations for no other reason than because it is right. We uphold honesty and ethical behavior and make good on our commitments. We understand that words and deeds matter and that integrity leads to trust.
• Community- Enables us to harness the power of our collective talents. We work together towards common goals. We recognize the importance of diversity where everyone's ideas, identities, backgrounds, and perspectives are valued and pave the paths that propel us forward. We understand our pioneering role in the broader scientific community and take pride in our efforts to have a positive impact on the world.
• Accountability - Keeps us focused, and keeps us honest. We are responsible not only for our own success, but the success of our teams and the entire Institute. We consider how the actions we take and the decisions we make in our own work may impact others.
• Respect - Creates the foundation of trust and brings out the best in us all. We value the experiences, identities, and feelings of those we work with, regardless of their position or their relationship to us. We provide feedback in a constructive manner, use appropriate language, and allow others to share their thoughts and ideas without fear of ridicule.
• Empowerment - Amplifies all voices and inspires the pursuit of greatness. We lift each other up, enabling us to grow continuously and live to our fullest potential. We support the expression of ideas, encourage self-advocacy, inspire confidence and recognize that an environment of mutual respect is critical to our collective success.

COMPETENCIES:

• Analytical - Synthesizes complex or diverse information; Collects and researches data; Uses intuition and experience to complement data; Designs workflows and procedures.
• Business Acumen - Understands business implications of decisions; Displays orientation to profitability; Demonstrates knowledge of market and competition; Aligns work with strategic goals.
• Change Management - Develops workable implementation plans; Communicates changes effectively; Builds commitment and overcomes resistance; Prepares and supports those affected by change; Monitors transition and evaluates results.
• Cost Consciousness - Works within approved budget; Develops and implements cost saving measures; Contributes to profits and revenue; Conserves organizational resources.
• Innovation - Displays original thinking and creativity; Meets challenges with resourcefulness; Generates suggestions for improving work; Develops innovative approaches and ideas; Presents ideas and information in a manner that gets others' attention.
• Judgement - Displays willingness to make decisions; Exhibits sound and accurate judgment; Supports and explains reasoning for decisions; Includes appropriate people in decision-making process; Makes timely decisions.
• Leadership - Exhibits confidence in self and others; Inspires and motivates others to perform well; Effectively influences actions and opinions of others; Accepts feedback from others; Gives appropriate recognition to others.
• ManagingPeople - Includes staff in planning, decision-making, facilitating and process improvement; Takes responsibility for subordinates' activities; Makes self available to staff; Provides regular performance feedback; Develops subordinates' skills and encourages growth; Solicits and applies customer feedback (internal and external); Fosters quality focus in others; Improves processes, products and services.; Continually works to improve supervisory skills.
• Oral Communication - Speaks clearly and persuasively in positive or negative situations; Listens and gets clarification; Responds well to questions; Demonstrates group presentation skills; Participates in meetings.
• Organizational Support - Follows policies and procedures; Completes administrative tasks correctly and on time; Supports organization's goals and values; Benefits organization through outside activities; Supports affirmative action and respects diversity.
• Planning/Organizing - Prioritizes and plans work activities; Uses time efficiently; Plans for additional resources; Sets goals and objectives; Organizes or schedules other people and their tasks; Develops realistic action plans.
• Problem Solving - Identifies and resolves problems in a timely manner; Gathers and analyzes information skillfully; Develops alternative solutions; Works well in group problem solving situations; Uses reason even when dealing with emotional topics.
• Project Management - Develops project plans; Coordinates projects; Communicates changes and progress; Completes projects on time and budget; Manages project team activities.
• Strategic Thinking - Develops strategies to achieve organizational goals; Understands organization's strengths & weaknesses; Analyzes market and competition; Identifies external threats and opportunities; Adapts strategy to changing conditions.
• Visionary Leadership - Displays passion and optimism; Inspires respect and trust; Mobilizes others to fulfill the vision; Provides vision and inspiration to peers and subordinates.
• Written Communication - Writes clearly and informatively; Edits work for spelling and grammar; Varies writing style to meet needs; Presents numerical data effectively; Able to read and interpret written information.
• Quality - Demonstrates accuracy and thoroughness; Looks for ways to improve and promote quality; Applies feedback to improve performance; Monitors own work to ensure quality.

The expected pay range for this position is $67,500-$88,750 per annum. Salk Institute provides pay ranges representing its good faith estimate of what the institute reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location, and external market pay for comparable jobs.
PHYSICAL DEMANDS AND WORK ENVIRONMENT:

• Occasionally required to stand
• Occasionally required to walk
• Continually required to sit
• Continually required to utilize hand and finger dexterity
• Frequently required to talk or hear
• Occasionally work near moving mechanical parts
• Occasionally work around fumes, airborne particles, or toxic chemicals
• Occasional exposure to bloodborne and airborne pathogens or infectious materials
• While performing the duties of this job, the noise level in the work environment is usually quiet.
• Specific vision abilities required by this job include: Close vision; Distance vision; Color vision; Peripheral vision; Depth perception and ability to adjust focus

The Salk Institute is an internationally renowned research institution that valuesdiversity, equity, and inclusion. We seek bold and interactive leaders passionate about exploring new frontiers in science. Our collaborative community embraces diverse perspectives and unique life experiences, fostering innovation, and a sense of belonging. Together, we strive to improve the wellbeing of humanity through groundbreaking research.
The above is intended to describe the general content of and requirements for the performance of this job. It is not to be construed as an exhaustive statement of duties, responsibilities, or physical requirements. Nothing in this job description restricts management's right to assign or reassign duties and responsibilities to this job at any time. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. All individuals who accept a position with the Salk Institute must be willing to work in an animal-related research environment, must successfully complete the Institute's background investigation and must be willing to sign a confidentiality agreement.
Equal Opportunity Employer/Protected Veterans/Individuals with Disabilities
The contractor will not discharge or in any other manner discriminate against employees or applicants because they have inquired about, discussed, or disclosed their own pay or the pay of another employee or applicant. However, employees who have access to the compensation information of other employees or applicants as a part of their essential job functions cannot disclose the pay of other employees or applicants to individuals who do not otherwise have access to compensation information, unless the disclosure is (a) in response to a formal complaint or charge, (b) in furtherance of an investigation, proceeding, hearing, or action, including an investigation conducted by the employer, or (c) consistent with the contractor's legal duty to furnish information. 41 CFR 60-1.35(c)