Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2021 / MWF 10:30 – 11:25 AM,  in Laufer Center rootm 101.

Recitations: Mon, 11:30 am – 12:30 pm, in Laufer Center Room 107.

Gabor Balazsi, Course PI

Course goals: The central idea of this course is the free energy, the quantitative way we understand thermodynamic forces driving the equilibria and transition rates in chemistry, physics and biology. We describe the components underpinning free energy: the entropy and internal energy. We explore the microscopic interactions - including hydrogen bonding, van der Waals interactions, electrostatics, and hydrophobic forces - that explain physical and chemical mechanisms in cell biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities form the basis for synthetic biology and drug discovery; coupled binding explains how biological machines convert energy and transduce signals or control gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules; with implications for molecular and cellular evolution.

Textbook:          Molecular Driving Forces by Dill & Bromberg. Garland Science, 2010

Extra textbook: Protein Actions by Bahar, Jernigan & Dill. Garland Science, 2017

Extra textbook: Physical Models of Living Systems. W. H. Freeman & Co., 2015

Prior years' course syllabi: 2020, 2019, 2018, 2017, 2016, 2015, 2014

{access public}Please login to get the links to the videos{/access}

MDF = Molecular Driving Forces, chapter numbers.
PA = Protein Actions, chapter numbers.

TAs:  TAs: Gregory Dignon, Christopher Foran.

For videos, please go to Blackboard.

Student Accessibility Support Center Statement
If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632- 6748, or via e-mail at:  This email address is being protected from spambots. You need JavaScript enabled to view it.. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential.

Academic Integrity Statement
Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school- specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html

Student Conduct and Community Standards
Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn.

Religious Observance
See the policy statement regarding religious holidays at here. Students are expected to notify the course professors by email of their intention to take time out for religious observance.  This should be done as soon as possible but definitely before the end of the add/drop period.  At that time they can discuss with the instructor(s) how they will be able to make up the work covered.

Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2022 / MWF 10:30 – 11:25 AM,  in Laufer Center rootm 101.

Recitations: Mon, 11:30 am – 12:30 pm, in Laufer Center Room 101.

Gabor Balazsi, Course PI

Course goals: The central idea of this course is the free energy, the quantitative way we understand thermodynamic forces driving the equilibria and transition rates in chemistry, physics and biology. We describe the components underpinning free energy: the entropy and internal energy. We explore the microscopic interactions - including hydrogen bonding, van der Waals interactions, electrostatics and hydrophobic forces - that explain physical and chemical mechanisms in cell biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities form the basis for synthetic biology and drug discovery; coupled binding explains how biological machines convert energy and transduce signals or control gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules; with implications for molecular and cellular evolution.

Textbook:          Molecular Driving Forces by Dill & Bromberg. Garland Science, 2010

Extra textbook: Protein Actions by Bahar, Jernigan & Dill. Garland Science, 2017

Extra textbook: Physical Models of Living Systems. W. H. Freeman & Co., 2015

Prior years' course syllabi: 2021, 2020, 2019, 2018, 2017, 2016, 2015, 2014

{access public}Please login to get the links to the videos{/access}

MDF = Molecular Driving Forces, chapter numbers.
PA = Protein Actions, chapter numbers.

TAs:  TAs: Jonathan Pachter(JP), Charles Kocher(CK).

For videos, please go to Blackboard.

Student Accessibility Support Center Statement
If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632- 6748, or via e-mail at:  This email address is being protected from spambots. You need JavaScript enabled to view it.. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential.

Academic Integrity Statement
Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school- specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html

Student Conduct and Community Standards
Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn.

Religious Observance
See the policy statement regarding religious holidays at here. Students are expected to notify the course professors by email of their intention to take time out for religious observance.  This should be done as soon as possible but definitely before the end of the add/drop period.  At that time they can discuss with the instructor(s) how they will be able to make up the work covered.

Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2018 / MWF 10 – 10:53 AM in Laufer Center 101

Recitations: Mon, 11:00 am – 12:00 pm in Laufer Center 107.

Gabor Balazsi, Course PI

Course goals: The central idea of this course is the free energy, the quantitative way we understand thermodynamic forces driving the equilibria and transition rates in chemistry, physics and biology. We describe the components underpinning free energy: the entropy and internal energy. We explore the microscopic interactions - including hydrogen bonding, van der Waals interactions, electrostatics and hydrophobic forces - that explain physical and chemical mechanisms in cell biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities form the basis for synthetic biology and drug discovery; coupled binding explains how biological machines convert energy and transduce signals or control gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules; with implications for molecular and cellular evolution.

Textbook:          Molecular Driving Forces by Dill & Bromberg. Garland Science, 2010

Extra textbook: Protein Actions by Bahar, Jernigan & Dill. Garland Science, 2017

Prior years' course syllabi: 2017, 2016, 2015, 2014

{access public}Please login to get the links to the videos{/access}

MDF = Molecular Driving Forces, chapter numbers.
PA = Protein Actions, chapter numbers.

TAs:  Luca Agozzino (#1 - #20), Roy Nassar (#21 - #36).

ACADEMIC INTEGRITY
Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person¹s work as your own is always wrong. Any suspected instance of academic dishonesty will be reported to the Academic Judiciary. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at http://www.stonybrook.edu/uaa/academicjudiciary/

ELECTRONIC COMMUNICATION
Email to your University email account is an important way of communicating with you for this course.  For most students the email address is This email address is being protected from spambots. You need JavaScript enabled to view it.¹, and the account can be accessed here: http://www.stonybrook.edu/mycloud.  *It is your responsibility to read your email received at this account.*

For instructions about how to verify your University email address see this: http://it.stonybrook.edu/help/kb/checking-or-changing-your-mail-forwarding-address-in-the-epo. You can set up email forwarding using instructions here: http://it.stonybrook.edu/help/kb/setting-up-mail-forwarding-in-google-mail. If you choose to forward your University email to another account, we are not responsible for any undeliverable messages.

RELIGIOUS OBSERVANCES
See the policy statement regarding religious holidays at http://www.stonybrook.edu/registrar/forms/RelHolPol%20081612%20cr.pdf. 

Students are expected to notify the course professors by email of their intention to take time out for religious observance.  This should be done as soon as possible but definitely before the end of the add/drop¹ period.  At that time they can discuss with the instructor(s) how they will be able to make up the work covered.

DISABILITIES
If you have a physical, psychiatric/emotional, medical or learning disability that may impact on your ability to carry out assigned course work, you should contact the staff in the Disability Support Services office [DSS], 632-6748/9. DSS will review your concerns and determine, with you, what accommodations are necessary and appropriate. All information and documentation of disability is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and Disability Support Services. For procedures and information go to the website: http://www.sunysb.edu/ehs/fire/disabilities.shtml.

CRITICAL INCIDENT MANAGEMENT
Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the University Police and the Office of University Community Standards any serious disruptive behavior that interrupts teaching, compromises the safety of the learning environment, and/or inhibits students¹ ability to learn. See more here: http://www.stonybrook.edu/sb/behavior.shtml

Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2017 / MWF 10 – 10:50 AM in Laufer Center 101

Gabor Balazsi, Course PI

Course goals: The central idea of this course is the free energy, the quantitative way we understand thermodynamic forces driving the equilibria and transition rates in chemistry, physics and biology. We describe the components underpinning free energy: the entropy and internal energy. We explore the microscopic interactions - including hydrogen bonding, van der Waals interactions, electrostatics and hydrophobic forces - that explain physical and chemical mechanisms in cell biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities form the basis for synthetic biology and drug discovery; coupled binding explains how biological machines convert energy and transduce signals or regulate gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules.

Textbook:          Molecular Driving Forces by Dill & Bromberg. Garland Science, 2010

Extra textbook: Protein Actions by Bahar, Jernigan & Dill. Garland Science, 2017

Prior years' course syllabi: 2016, 2015, 2014

{access public}Please login to get the links to the videos{/access}

MDF = Molecular Driving Forces, chapter numbers.
PA = Protein Actions, chapter numbers.

TAs: Michael Cortes (#1 - #20). Chuan Tian, Bihua Yu and Cong Liu (#21 - #36).

ACADEMIC INTEGRITY
Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person¹s work as your own is always wrong. Any suspected instance of academic dishonesty will be reported to the Academic Judiciary. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at http://www.stonybrook.edu/uaa/academicjudiciary/

ELECTRONIC COMMUNICATION
Email to your University email account is an important way of communicating with you for this course.  For most students the email address is This email address is being protected from spambots. You need JavaScript enabled to view it.¹, and the account can be accessed here: http://www.stonybrook.edu/mycloud.  *It is your responsibility to read your email received at this account.*

For instructions about how to verify your University email address see this: http://it.stonybrook.edu/help/kb/checking-or-changing-your-mail-forwarding-address-in-the-epo. You can set up email forwarding using instructions here: http://it.stonybrook.edu/help/kb/setting-up-mail-forwarding-in-google-mail. If you choose to forward your University email to another account, we are not responsible for any undeliverable messages.

RELIGIOUS OBSERVANCES
See the policy statement regarding religious holidays at http://www.stonybrook.edu/registrar/forms/RelHolPol%20081612%20cr.pdf. 

Students are expected to notify the course professors by email of their intention to take time out for religious observance.  This should be done as soon as possible but definitely before the end of the add/drop¹ period.  At that time they can discuss with the instructor(s) how they will be able to make up the work covered.

DISABILITIES
If you have a physical, psychiatric/emotional, medical or learning disability that may impact on your ability to carry out assigned course work, you should contact the staff in the Disability Support Services office [DSS], 632-6748/9. DSS will review your concerns and determine, with you, what accommodations are necessary and appropriate. All information and documentation of disability is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and Disability Support Services. For procedures and information go to the website: http://www.sunysb.edu/ehs/fire/disabilities.shtml.

CRITICAL INCIDENT MANAGEMENT
Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the University Police and the Office of University Community Standards any serious disruptive behavior that interrupts teaching, compromises the safety of the learning environment, and/or inhibits students¹ ability to learn. See more here: http://www.stonybrook.edu/sb/behavior.shtml